diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1011f64d71..fe8ccf0caa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ All notable changes to this project are documented in this file.
 ### Changed
 - 🤖 [ergoCubSN001] Add logging of the wrist and fix the name of the waist imu (https://github.com/ami-iit/bipedal-locomotion-framework/pull/810)
 - Export the CoM velocity and the angular momentum trajectory in the `CentroidalMPC` (https://github.com/ami-iit/bipedal-locomotion-framework/pull/818)
+- Require `iDynTree v10.0.0` (https://github.com/ami-iit/bipedal-locomotion-framework/pull/832)
 
 ### Fixed
 - Fix the barrier logic for threads synchronization (https://github.com/ami-iit/bipedal-locomotion-framework/pull/811)
diff --git a/bindings/python/Conversions/src/ManifConversions.cpp b/bindings/python/Conversions/src/ManifConversions.cpp
index d03fbc94ea..e50ef0fc09 100644
--- a/bindings/python/Conversions/src/ManifConversions.cpp
+++ b/bindings/python/Conversions/src/ManifConversions.cpp
@@ -10,8 +10,8 @@
 
 #include <Eigen/Dense>
 
-#include <iDynTree/Core/Rotation.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/Rotation.h>
+#include <iDynTree/Transform.h>
 
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <BipedalLocomotion/bindings/type_caster/swig.h>
diff --git a/bindings/python/ML/src/MANNAutoregressive.cpp b/bindings/python/ML/src/MANNAutoregressive.cpp
index 6dcc4d4011..5ca40ea7b3 100644
--- a/bindings/python/ML/src/MANNAutoregressive.cpp
+++ b/bindings/python/ML/src/MANNAutoregressive.cpp
@@ -5,7 +5,7 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 #include <pybind11/eigen.h>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
diff --git a/bindings/python/ML/src/MANNAutoregressiveInputBuilder.cpp b/bindings/python/ML/src/MANNAutoregressiveInputBuilder.cpp
index df4a45834d..003bb64d9f 100644
--- a/bindings/python/ML/src/MANNAutoregressiveInputBuilder.cpp
+++ b/bindings/python/ML/src/MANNAutoregressiveInputBuilder.cpp
@@ -5,7 +5,7 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 #include <pybind11/chrono.h>
 #include <pybind11/eigen.h>
 #include <pybind11/pybind11.h>
diff --git a/bindings/python/ML/src/MANNTrajectoryGenerator.cpp b/bindings/python/ML/src/MANNTrajectoryGenerator.cpp
index 36b38f52a7..eaa153162b 100644
--- a/bindings/python/ML/src/MANNTrajectoryGenerator.cpp
+++ b/bindings/python/ML/src/MANNTrajectoryGenerator.cpp
@@ -5,7 +5,7 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 #include <pybind11/chrono.h>
 #include <pybind11/eigen.h>
 #include <pybind11/pybind11.h>
diff --git a/bindings/python/RobotDynamicsEstimator/src/RobotDynamicsEstimator.cpp b/bindings/python/RobotDynamicsEstimator/src/RobotDynamicsEstimator.cpp
index 23caee3efb..4ad6b1402d 100644
--- a/bindings/python/RobotDynamicsEstimator/src/RobotDynamicsEstimator.cpp
+++ b/bindings/python/RobotDynamicsEstimator/src/RobotDynamicsEstimator.cpp
@@ -9,7 +9,7 @@
 #include <pybind11/eigen.h>
 #include <pybind11/stl.h>
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 
 #include <BipedalLocomotion/System/Advanceable.h>
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
diff --git a/bindings/python/TSID/src/JointDynamicsTask.cpp b/bindings/python/TSID/src/JointDynamicsTask.cpp
index b85a6097dc..1150cfbd10 100644
--- a/bindings/python/TSID/src/JointDynamicsTask.cpp
+++ b/bindings/python/TSID/src/JointDynamicsTask.cpp
@@ -5,7 +5,7 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Model/JointState.h>
+#include <iDynTree/JointState.h>
 #include <pybind11/eigen.h>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
diff --git a/cmake/BipedalLocomotionFrameworkDependencies.cmake b/cmake/BipedalLocomotionFrameworkDependencies.cmake
index ea6edc97e1..4a563f6848 100644
--- a/cmake/BipedalLocomotionFrameworkDependencies.cmake
+++ b/cmake/BipedalLocomotionFrameworkDependencies.cmake
@@ -17,8 +17,8 @@ endif()
 ################################################################################
 ########################## Mandatory dependencies ##############################
 
-find_package(iDynTree 3.0.0 REQUIRED)
-dependency_classifier(iDynTree MINIMUM_VERSION 3.0.0 IS_USED TRUE PUBLIC)
+find_package(iDynTree 10.0.0 REQUIRED)
+dependency_classifier(iDynTree MINIMUM_VERSION 10.0.0 IS_USED TRUE PUBLIC)
 
 find_package(Eigen3 3.2.92 REQUIRED)
 dependency_classifier(Eigen3 MINIMUM_VERSION 3.2.92 IS_USED TRUE PUBLIC)
diff --git a/devices/FloatingBaseEstimatorDevice/include/BipedalLocomotion/FloatingBaseEstimatorDevice.h b/devices/FloatingBaseEstimatorDevice/include/BipedalLocomotion/FloatingBaseEstimatorDevice.h
index aa20b1d0cb..730735351d 100644
--- a/devices/FloatingBaseEstimatorDevice/include/BipedalLocomotion/FloatingBaseEstimatorDevice.h
+++ b/devices/FloatingBaseEstimatorDevice/include/BipedalLocomotion/FloatingBaseEstimatorDevice.h
@@ -13,7 +13,7 @@
 #include <BipedalLocomotion/FloatingBaseEstimators/FloatingBaseEstimator.h>
 
 #include <iDynTree/Estimation/ContactStateMachine.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <yarp/os/PeriodicThread.h>
 #include <yarp/dev/DeviceDriver.h>
diff --git a/devices/FloatingBaseEstimatorDevice/src/FloatingBaseEstimatorDevice.cpp b/devices/FloatingBaseEstimatorDevice/src/FloatingBaseEstimatorDevice.cpp
index 8b1ad51797..6c1ca9f728 100644
--- a/devices/FloatingBaseEstimatorDevice/src/FloatingBaseEstimatorDevice.cpp
+++ b/devices/FloatingBaseEstimatorDevice/src/FloatingBaseEstimatorDevice.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/YarpUtilities/Helper.h>
 
 #include <BipedalLocomotion/FloatingBaseEstimators/InvariantEKFBaseEstimator.h>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/yarp/YARPConversions.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/YARPConversions.h>
 #include <yarp/os/LogStream.h>
 
 using namespace BipedalLocomotion;
diff --git a/devices/RobotDynamicsEstimatorDevice/include/BipedalLocomotion/RobotDynamicsEstimatorDevice.h b/devices/RobotDynamicsEstimatorDevice/include/BipedalLocomotion/RobotDynamicsEstimatorDevice.h
index 03529c6579..a6157fda17 100644
--- a/devices/RobotDynamicsEstimatorDevice/include/BipedalLocomotion/RobotDynamicsEstimatorDevice.h
+++ b/devices/RobotDynamicsEstimatorDevice/include/BipedalLocomotion/RobotDynamicsEstimatorDevice.h
@@ -18,7 +18,7 @@
 
 #include <iDynTree/Estimation/ContactStateMachine.h>
 #include <iDynTree/Estimation/ExtWrenchesAndJointTorquesEstimator.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <yarp/dev/DeviceDriver.h>
 #include <yarp/dev/IFrameTransform.h>
diff --git a/devices/RobotDynamicsEstimatorDevice/src/RobotDynamicsEstimatorDevice.cpp b/devices/RobotDynamicsEstimatorDevice/src/RobotDynamicsEstimatorDevice.cpp
index 7b171e70ef..948856917f 100644
--- a/devices/RobotDynamicsEstimatorDevice/src/RobotDynamicsEstimatorDevice.cpp
+++ b/devices/RobotDynamicsEstimatorDevice/src/RobotDynamicsEstimatorDevice.cpp
@@ -10,8 +10,8 @@
 #include <BipedalLocomotion/System/Clock.h>
 #include <BipedalLocomotion/YarpUtilities/Helper.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/yarp/YARPConversions.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/YARPConversions.h>
 #include <yarp/eigen/Eigen.h>
 
 using namespace BipedalLocomotion;
diff --git a/src/ContactModels/include/BipedalLocomotion/ContactModels/ContactModel.h b/src/ContactModels/include/BipedalLocomotion/ContactModels/ContactModel.h
index 3bbfbe3512..20f2e64295 100644
--- a/src/ContactModels/include/BipedalLocomotion/ContactModels/ContactModel.h
+++ b/src/ContactModels/include/BipedalLocomotion/ContactModels/ContactModel.h
@@ -13,12 +13,12 @@
 #include <string>
 #include <unordered_map>
 
-#include <iDynTree/Core/MatrixDynSize.h>
-#include <iDynTree/Core/MatrixFixSize.h>
-#include <iDynTree/Core/Transform.h>
-#include <iDynTree/Core/Twist.h>
-#include <iDynTree/Core/VectorFixSize.h>
-#include <iDynTree/Core/Wrench.h>
+#include <iDynTree/MatrixDynSize.h>
+#include <iDynTree/MatrixFixSize.h>
+#include <iDynTree/Transform.h>
+#include <iDynTree/Twist.h>
+#include <iDynTree/VectorFixSize.h>
+#include <iDynTree/Wrench.h>
 
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
 
diff --git a/src/ContactModels/include/BipedalLocomotion/ContactModels/ContinuousContactModel.h b/src/ContactModels/include/BipedalLocomotion/ContactModels/ContinuousContactModel.h
index d4ccce2af8..193ec88657 100644
--- a/src/ContactModels/include/BipedalLocomotion/ContactModels/ContinuousContactModel.h
+++ b/src/ContactModels/include/BipedalLocomotion/ContactModels/ContinuousContactModel.h
@@ -8,9 +8,9 @@
 #ifndef BIPEDAL_LOCOMOTION_CONTACT_MODELS_CONTINUOUS_CONTACT_MODEL_H
 #define BIPEDAL_LOCOMOTION_CONTACT_MODELS_CONTINUOUS_CONTACT_MODEL_H
 
-#include <iDynTree/Core/Transform.h>
-#include <iDynTree/Core/Twist.h>
-#include <iDynTree/Core/Wrench.h>
+#include <iDynTree/Transform.h>
+#include <iDynTree/Twist.h>
+#include <iDynTree/Wrench.h>
 
 #include <BipedalLocomotion/ContactModels/ContactModel.h>
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
diff --git a/src/ContactModels/src/ContinuousContactModel.cpp b/src/ContactModels/src/ContinuousContactModel.cpp
index 7c11760ce7..ac9c86fee3 100644
--- a/src/ContactModels/src/ContinuousContactModel.cpp
+++ b/src/ContactModels/src/ContinuousContactModel.cpp
@@ -5,7 +5,7 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 #include <BipedalLocomotion/ContactModels/ContinuousContactModel.h>
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
diff --git a/src/ContactModels/tests/ContinousContactModelTest.cpp b/src/ContactModels/tests/ContinousContactModelTest.cpp
index ab260851ac..f86fedf712 100644
--- a/src/ContactModels/tests/ContinousContactModelTest.cpp
+++ b/src/ContactModels/tests/ContinousContactModelTest.cpp
@@ -10,8 +10,8 @@
 // Catch2
 #include <catch2/catch_test_macros.hpp>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/SpatialAcc.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/SpatialAcc.h>
 
 #include <BipedalLocomotion/ContactModels/ContinuousContactModel.h>
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
diff --git a/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/CompliantContactWrench.h b/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/CompliantContactWrench.h
index 9611400fc1..3f3353be61 100644
--- a/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/CompliantContactWrench.h
+++ b/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/CompliantContactWrench.h
@@ -11,7 +11,7 @@
 #include <memory>
 
 #include <BipedalLocomotion/ContactModels/ContactModel.h>
-#include <iDynTree/Model/Indices.h>
+#include <iDynTree/Indices.h>
 
 namespace BipedalLocomotion
 {
diff --git a/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/ForwardEuler.h b/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/ForwardEuler.h
index ce0c788c43..24313f864b 100644
--- a/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/ForwardEuler.h
+++ b/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/ForwardEuler.h
@@ -12,7 +12,7 @@
 #include <tuple>
 #include <type_traits>
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 #include <BipedalLocomotion/ContinuousDynamicalSystem/FixedStepIntegrator.h>
 #include <BipedalLocomotion/GenericContainer/NamedTuple.h>
diff --git a/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/RK4.h b/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/RK4.h
index 3bf2eb29ed..b198057017 100644
--- a/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/RK4.h
+++ b/src/ContinuousDynamicalSystem/include/BipedalLocomotion/ContinuousDynamicalSystem/RK4.h
@@ -12,7 +12,7 @@
 #include <tuple>
 #include <type_traits>
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 #include <BipedalLocomotion/ContinuousDynamicalSystem/FixedStepIntegrator.h>
 #include <BipedalLocomotion/GenericContainer/NamedTuple.h>
diff --git a/src/ContinuousDynamicalSystem/src/FixedBaseDynamics.cpp b/src/ContinuousDynamicalSystem/src/FixedBaseDynamics.cpp
index bc6e3a524f..cf45a1f4ff 100644
--- a/src/ContinuousDynamicalSystem/src/FixedBaseDynamics.cpp
+++ b/src/ContinuousDynamicalSystem/src/FixedBaseDynamics.cpp
@@ -5,9 +5,9 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Core/Twist.h>
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/Twist.h>
+#include <iDynTree/EigenHelpers.h>
 
 #include <BipedalLocomotion/ContinuousDynamicalSystem/FixedBaseDynamics.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
diff --git a/src/ContinuousDynamicalSystem/src/FloatingBaseDynamicsWithCompliantContacts.cpp b/src/ContinuousDynamicalSystem/src/FloatingBaseDynamicsWithCompliantContacts.cpp
index 72122c87e8..6f7d171d0d 100644
--- a/src/ContinuousDynamicalSystem/src/FloatingBaseDynamicsWithCompliantContacts.cpp
+++ b/src/ContinuousDynamicalSystem/src/FloatingBaseDynamicsWithCompliantContacts.cpp
@@ -5,9 +5,9 @@
  * distributed under the terms of the BSD-3-Clause license.
  */
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/Twist.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Twist.h>
+#include <iDynTree/Model.h>
 
 #include <BipedalLocomotion/ContinuousDynamicalSystem/FloatingBaseDynamicsWithCompliantContacts.h>
 #include <BipedalLocomotion/Conversions/CommonConversions.h>
diff --git a/src/Conversions/include/BipedalLocomotion/Conversions/ManifConversions.h b/src/Conversions/include/BipedalLocomotion/Conversions/ManifConversions.h
index 69a07aabd7..cfeb820cc2 100644
--- a/src/Conversions/include/BipedalLocomotion/Conversions/ManifConversions.h
+++ b/src/Conversions/include/BipedalLocomotion/Conversions/ManifConversions.h
@@ -8,9 +8,9 @@
 #ifndef BIPEDAL_LOCOMOTION_MANIF_CONVERSIONS_H
 #define BIPEDAL_LOCOMOTION_MANIF_CONVERSIONS_H
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/Transform.h>
-#include <iDynTree/Core/Twist.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Transform.h>
+#include <iDynTree/Twist.h>
 
 #include <manif/manif.h>
 
diff --git a/src/Conversions/include/BipedalLocomotion/Conversions/matioCppConversions.h b/src/Conversions/include/BipedalLocomotion/Conversions/matioCppConversions.h
index db9ce74c1a..7997a88937 100644
--- a/src/Conversions/include/BipedalLocomotion/Conversions/matioCppConversions.h
+++ b/src/Conversions/include/BipedalLocomotion/Conversions/matioCppConversions.h
@@ -9,9 +9,9 @@
 #define BIPEDAL_LOCOMOTION_MATIOCPPCONVERSIONS_H
 
 #include <Eigen/Core>
-#include <iDynTree/Core/MatrixDynSize.h>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/MatrixFixSize.h>
+#include <iDynTree/MatrixDynSize.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/MatrixFixSize.h>
 #include <matioCpp/matioCpp.h>
 #include <BipedalLocomotion/GenericContainer/Vector.h>
 
diff --git a/src/Conversions/tests/ManifConversionsTest.cpp b/src/Conversions/tests/ManifConversionsTest.cpp
index 9f51414ff7..4ccd13f1d9 100644
--- a/src/Conversions/tests/ManifConversionsTest.cpp
+++ b/src/Conversions/tests/ManifConversionsTest.cpp
@@ -10,7 +10,7 @@
 
 #include <BipedalLocomotion/Conversions/CommonConversions.h>
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 TEST_CASE("Manif Conversions")
 {
diff --git a/src/Conversions/tests/matioCppConversionsTest.cpp b/src/Conversions/tests/matioCppConversionsTest.cpp
index 5d14aa2f2f..cf2b678527 100644
--- a/src/Conversions/tests/matioCppConversionsTest.cpp
+++ b/src/Conversions/tests/matioCppConversionsTest.cpp
@@ -8,7 +8,7 @@
 // Catch2
 #include <catch2/catch_test_macros.hpp>
 #include <BipedalLocomotion/Conversions/matioCppConversions.h>
-#include <iDynTree/Core/VectorDynSize.h>
+#include <iDynTree/VectorDynSize.h>
 #include <unordered_map>
 #include <map>
 #include <set>
diff --git a/src/Estimators/include/BipedalLocomotion/FloatingBaseEstimators/BaseEstimatorFromFootIMU.h b/src/Estimators/include/BipedalLocomotion/FloatingBaseEstimators/BaseEstimatorFromFootIMU.h
index 22abc4998d..769855442d 100644
--- a/src/Estimators/include/BipedalLocomotion/FloatingBaseEstimators/BaseEstimatorFromFootIMU.h
+++ b/src/Estimators/include/BipedalLocomotion/FloatingBaseEstimators/BaseEstimatorFromFootIMU.h
@@ -12,7 +12,7 @@
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
 #include <BipedalLocomotion/System/Advanceable.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 #include <manif/SE3.h>
 #include <manif/SO3.h>
 
diff --git a/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/KinDynWrapper.h b/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/KinDynWrapper.h
index 5aeb142473..5f834a4851 100644
--- a/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/KinDynWrapper.h
+++ b/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/KinDynWrapper.h
@@ -11,7 +11,7 @@
 #include <map>
 
 // iDynTree
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 #include <iDynTree/KinDynComputations.h>
 
 // Eigen
diff --git a/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/SubModel.h b/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/SubModel.h
index 6686e081eb..f2c6ac521c 100644
--- a/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/SubModel.h
+++ b/src/Estimators/include/BipedalLocomotion/RobotDynamicsEstimator/SubModel.h
@@ -15,8 +15,8 @@
 
 // iDynTree
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelLoader.h>
 
 // BLF
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
diff --git a/src/Estimators/src/FloatingBaseEstimator.cpp b/src/Estimators/src/FloatingBaseEstimator.cpp
index 24636fe219..87521ed7ac 100755
--- a/src/Estimators/src/FloatingBaseEstimator.cpp
+++ b/src/Estimators/src/FloatingBaseEstimator.cpp
@@ -11,7 +11,7 @@
 
 #include <chrono>
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion;
 using namespace BipedalLocomotion::Estimators;
diff --git a/src/Estimators/src/InvariantEKFBaseEstimator.cpp b/src/Estimators/src/InvariantEKFBaseEstimator.cpp
index 65f55de237..a8a3824b06 100644
--- a/src/Estimators/src/InvariantEKFBaseEstimator.cpp
+++ b/src/Estimators/src/InvariantEKFBaseEstimator.cpp
@@ -6,7 +6,7 @@
  */
 
 #include <BipedalLocomotion/FloatingBaseEstimators/InvariantEKFBaseEstimator.h>
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 #include <manif/manif.h>
 
diff --git a/src/Estimators/src/KinDynWrapper.cpp b/src/Estimators/src/KinDynWrapper.cpp
index f6c36ef4e9..d3cc614154 100644
--- a/src/Estimators/src/KinDynWrapper.cpp
+++ b/src/Estimators/src/KinDynWrapper.cpp
@@ -7,9 +7,9 @@
 
 #include <Eigen/QR>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/MatrixView.h>
-#include <iDynTree/Core/Span.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/MatrixView.h>
+#include <iDynTree/Span.h>
 
 // BLF
 #include <BipedalLocomotion/RobotDynamicsEstimator/KinDynWrapper.h>
diff --git a/src/Estimators/src/LeggedOdometry.cpp b/src/Estimators/src/LeggedOdometry.cpp
index 996d12e4c5..359e6e45fc 100755
--- a/src/Estimators/src/LeggedOdometry.cpp
+++ b/src/Estimators/src/LeggedOdometry.cpp
@@ -8,8 +8,8 @@
 #include <BipedalLocomotion/FloatingBaseEstimators/LeggedOdometry.h>
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <chrono>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 #include <manif/manif.h>
 
 using namespace BipedalLocomotion::Estimators;
diff --git a/src/Estimators/src/SubModel.cpp b/src/Estimators/src/SubModel.cpp
index 5b32af7f4f..916e65490a 100644
--- a/src/Estimators/src/SubModel.cpp
+++ b/src/Estimators/src/SubModel.cpp
@@ -6,10 +6,10 @@
  */
 
 // iDyn
-#include <iDynTree/Model/SubModel.h>
-#include <iDynTree/Model/Traversal.h>
-#include <iDynTree/Model/ModelTransformers.h>
-#include <iDynTree/Sensors/SixAxisForceTorqueSensor.h>
+#include <iDynTree/SubModel.h>
+#include <iDynTree/Traversal.h>
+#include <iDynTree/ModelTransformers.h>
+#include <iDynTree/SixAxisForceTorqueSensor.h>
 
 // BLF
 #include <BipedalLocomotion/TextLogging/Logger.h>
diff --git a/src/Estimators/tests/FloatingBaseEstimators/BaseEstimatorFromFootIMUTest.cpp b/src/Estimators/tests/FloatingBaseEstimators/BaseEstimatorFromFootIMUTest.cpp
index 2a76cf8db8..298229f146 100644
--- a/src/Estimators/tests/FloatingBaseEstimators/BaseEstimatorFromFootIMUTest.cpp
+++ b/src/Estimators/tests/FloatingBaseEstimators/BaseEstimatorFromFootIMUTest.cpp
@@ -11,8 +11,8 @@
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 #include <iCubModels/iCubModels.h>
-#include <iDynTree/Core/TestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/TestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <Eigen/Dense>
 #include <catch2/catch_test_macros.hpp>
diff --git a/src/Estimators/tests/FloatingBaseEstimators/FloatingBaseEstimatorTest.cpp b/src/Estimators/tests/FloatingBaseEstimators/FloatingBaseEstimatorTest.cpp
index 13dc1d02d3..b15cc373a8 100644
--- a/src/Estimators/tests/FloatingBaseEstimators/FloatingBaseEstimatorTest.cpp
+++ b/src/Estimators/tests/FloatingBaseEstimators/FloatingBaseEstimatorTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 
-#include <iDynTree/Core/TestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/TestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <iCubModels/iCubModels.h>
 
diff --git a/src/Estimators/tests/FloatingBaseEstimators/InvariantEKFBaseEstimatorTest.cpp b/src/Estimators/tests/FloatingBaseEstimators/InvariantEKFBaseEstimatorTest.cpp
index ecb0589e3e..141140497a 100644
--- a/src/Estimators/tests/FloatingBaseEstimators/InvariantEKFBaseEstimatorTest.cpp
+++ b/src/Estimators/tests/FloatingBaseEstimators/InvariantEKFBaseEstimatorTest.cpp
@@ -16,11 +16,11 @@
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/TestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/TestUtils.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/ModelLoader.h>
+#include <iDynTree/Model.h>
 
 #include <iCubModels/iCubModels.h>
 
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/AccelerometerMeasurementDynamicsTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/AccelerometerMeasurementDynamicsTest.cpp
index 2572a5ad25..b562119ed0 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/AccelerometerMeasurementDynamicsTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/AccelerometerMeasurementDynamicsTest.cpp
@@ -12,10 +12,10 @@
 #include <yarp/os/ResourceFinder.h>
 
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Model/ModelTestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelTestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <BipedalLocomotion/Math/Constants.h>
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/FrictionTorqueStateDynamicsTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/FrictionTorqueStateDynamicsTest.cpp
index e633ba9493..593b4bc435 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/FrictionTorqueStateDynamicsTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/FrictionTorqueStateDynamicsTest.cpp
@@ -13,8 +13,8 @@
 #include <yarp/os/ResourceFinder.h>
 
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <BipedalLocomotion/Math/Constants.h>
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/GyroscopeMeasurementDynamicsTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/GyroscopeMeasurementDynamicsTest.cpp
index 65cc8ddeda..e5b11c7c1c 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/GyroscopeMeasurementDynamicsTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/GyroscopeMeasurementDynamicsTest.cpp
@@ -12,10 +12,10 @@
 #include <yarp/os/ResourceFinder.h>
 
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Model/ModelTestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelTestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <BipedalLocomotion/Math/Constants.h>
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/JointVelocityStateDynamicsTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/JointVelocityStateDynamicsTest.cpp
index ec60c0e83a..1fc7904e25 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/JointVelocityStateDynamicsTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/JointVelocityStateDynamicsTest.cpp
@@ -13,10 +13,10 @@
 #include <yarp/os/ResourceFinder.h>
 
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Model/ModelTestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelTestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <BipedalLocomotion/Math/Constants.h>
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/KinDynWrapperTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/KinDynWrapperTest.cpp
index c6248aef78..e1b072bc10 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/KinDynWrapperTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/KinDynWrapperTest.cpp
@@ -12,10 +12,10 @@
 #include <yarp/os/ResourceFinder.h>
 
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Model/ModelTestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelTestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <BipedalLocomotion/Math/Constants.h>
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/RobotDynamicsEstimationTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/RobotDynamicsEstimationTest.cpp
index 7aadbb14e1..8b3397e377 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/RobotDynamicsEstimationTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/RobotDynamicsEstimationTest.cpp
@@ -15,10 +15,10 @@
 #include <ConfigFolderPath.h>
 
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Model/FreeFloatingState.h>
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Model/ModelTestUtils.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/FreeFloatingState.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelTestUtils.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <BipedalLocomotion/Conversions/ManifConversions.h>
 #include <BipedalLocomotion/Conversions/matioCppConversions.h>
diff --git a/src/Estimators/tests/RobotDynamicsEstimator/SubModelCreatorTest.cpp b/src/Estimators/tests/RobotDynamicsEstimator/SubModelCreatorTest.cpp
index a290efe9f1..6e4a5ac065 100644
--- a/src/Estimators/tests/RobotDynamicsEstimator/SubModelCreatorTest.cpp
+++ b/src/Estimators/tests/RobotDynamicsEstimator/SubModelCreatorTest.cpp
@@ -20,7 +20,7 @@
 
 // iDynTree
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/ModelLoader.h>
 
 #include <ConfigFolderPath.h>
 
diff --git a/src/GenericContainer/include/BipedalLocomotion/GenericContainer/Vector.h b/src/GenericContainer/include/BipedalLocomotion/GenericContainer/Vector.h
index 440bda3f52..625dc6f2ca 100644
--- a/src/GenericContainer/include/BipedalLocomotion/GenericContainer/Vector.h
+++ b/src/GenericContainer/include/BipedalLocomotion/GenericContainer/Vector.h
@@ -9,7 +9,7 @@
 #define BIPEDAL_LOCOMOTION_GENERIC_CONTAINER_VECTOR_H
 
 // iDynTree
-#include <iDynTree/Core/Span.h>
+#include <iDynTree/Span.h>
 
 // Template helpers
 #include <BipedalLocomotion/GenericContainer/TemplateHelpers.h>
diff --git a/src/GenericContainer/tests/GenericContainerTest.cpp b/src/GenericContainer/tests/GenericContainerTest.cpp
index f11f131ac5..913a784102 100644
--- a/src/GenericContainer/tests/GenericContainerTest.cpp
+++ b/src/GenericContainer/tests/GenericContainerTest.cpp
@@ -7,10 +7,10 @@
 
 // Catch2
 #include <catch2/catch_test_macros.hpp>
-#include <iDynTree/Core/VectorDynSize.h>
-#include <iDynTree/Core/VectorFixSize.h>
-#include <iDynTree/Core/TestUtils.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/VectorDynSize.h>
+#include <iDynTree/VectorFixSize.h>
+#include <iDynTree/TestUtils.h>
+#include <iDynTree/Transform.h>
 #include <memory>
 #include <vector>
 #include <string>
diff --git a/src/GenericContainer/tests/GenericContainerTestPlusYarp.cpp b/src/GenericContainer/tests/GenericContainerTestPlusYarp.cpp
index 6abb944fdd..d1ad513282 100644
--- a/src/GenericContainer/tests/GenericContainerTestPlusYarp.cpp
+++ b/src/GenericContainer/tests/GenericContainerTestPlusYarp.cpp
@@ -7,9 +7,9 @@
 
 // Catch2
 #include <catch2/catch_test_macros.hpp>
-#include <iDynTree/Core/VectorDynSize.h>
-#include <iDynTree/Core/VectorFixSize.h>
-#include <iDynTree/Core/TestUtils.h>
+#include <iDynTree/VectorDynSize.h>
+#include <iDynTree/VectorFixSize.h>
+#include <iDynTree/TestUtils.h>
 
 #include <yarp/sig/Vector.h>
 
diff --git a/src/IK/src/AngularMomentumTask.cpp b/src/IK/src/AngularMomentumTask.cpp
index 8d52bfe1ea..5038ce76ec 100644
--- a/src/IK/src/AngularMomentumTask.cpp
+++ b/src/IK/src/AngularMomentumTask.cpp
@@ -8,8 +8,8 @@
 #include <BipedalLocomotion/IK/AngularMomentumTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/src/CoMTask.cpp b/src/IK/src/CoMTask.cpp
index 02fb4a7b12..21bd9e42ec 100644
--- a/src/IK/src/CoMTask.cpp
+++ b/src/IK/src/CoMTask.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/IK/CoMTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/src/DistanceTask.cpp b/src/IK/src/DistanceTask.cpp
index 67c6eb3fa2..0a5ef73572 100644
--- a/src/IK/src/DistanceTask.cpp
+++ b/src/IK/src/DistanceTask.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/IK/DistanceTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/src/GravityTask.cpp b/src/IK/src/GravityTask.cpp
index 7de70b466f..f4a1aa0da6 100644
--- a/src/IK/src/GravityTask.cpp
+++ b/src/IK/src/GravityTask.cpp
@@ -8,8 +8,8 @@
 #include <BipedalLocomotion/IK/GravityTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/src/JointLimitsTask.cpp b/src/IK/src/JointLimitsTask.cpp
index c0a839024e..71316e24ff 100644
--- a/src/IK/src/JointLimitsTask.cpp
+++ b/src/IK/src/JointLimitsTask.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/IK/JointLimitsTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::IK;
diff --git a/src/IK/src/JointTrackingTask.cpp b/src/IK/src/JointTrackingTask.cpp
index cf3f79e0ab..e9e5c864c9 100644
--- a/src/IK/src/JointTrackingTask.cpp
+++ b/src/IK/src/JointTrackingTask.cpp
@@ -9,7 +9,7 @@
 
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::IK;
diff --git a/src/IK/src/R3Task.cpp b/src/IK/src/R3Task.cpp
index 17afbfb85b..91f3124013 100644
--- a/src/IK/src/R3Task.cpp
+++ b/src/IK/src/R3Task.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/IK/R3Task.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/src/SE3Task.cpp b/src/IK/src/SE3Task.cpp
index 78949d593a..29dcde1e43 100644
--- a/src/IK/src/SE3Task.cpp
+++ b/src/IK/src/SE3Task.cpp
@@ -11,8 +11,8 @@
 
 #include <Eigen/src/Geometry/Quaternion.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/src/SO3Task.cpp b/src/IK/src/SO3Task.cpp
index 3a65014b7f..441b08dea0 100644
--- a/src/IK/src/SO3Task.cpp
+++ b/src/IK/src/SO3Task.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/IK/SO3Task.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/AngularMomentumTaskTest.cpp b/src/IK/tests/AngularMomentumTaskTest.cpp
index 7738f21fbc..ece6fc4832 100644
--- a/src/IK/tests/AngularMomentumTaskTest.cpp
+++ b/src/IK/tests/AngularMomentumTaskTest.cpp
@@ -13,8 +13,8 @@
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 #include <BipedalLocomotion/System/VariablesHandler.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/CoMTaskTest.cpp b/src/IK/tests/CoMTaskTest.cpp
index b97e0b3b8c..75f8b0ce86 100644
--- a/src/IK/tests/CoMTaskTest.cpp
+++ b/src/IK/tests/CoMTaskTest.cpp
@@ -14,8 +14,8 @@
 
 #include <BipedalLocomotion/IK/CoMTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/DistanceTaskTest.cpp b/src/IK/tests/DistanceTaskTest.cpp
index 0d12ae98cd..3bae3dc3ed 100644
--- a/src/IK/tests/DistanceTaskTest.cpp
+++ b/src/IK/tests/DistanceTaskTest.cpp
@@ -13,8 +13,8 @@
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 #include <BipedalLocomotion/System/VariablesHandler.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/IK/tests/GravityTaskTest.cpp b/src/IK/tests/GravityTaskTest.cpp
index 38837130e5..afe0081e38 100644
--- a/src/IK/tests/GravityTaskTest.cpp
+++ b/src/IK/tests/GravityTaskTest.cpp
@@ -13,8 +13,8 @@
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 #include <BipedalLocomotion/System/VariablesHandler.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/IK/tests/JointLimitsTaskTest.cpp b/src/IK/tests/JointLimitsTaskTest.cpp
index 46bcf9f160..bd47f0c103 100644
--- a/src/IK/tests/JointLimitsTaskTest.cpp
+++ b/src/IK/tests/JointLimitsTaskTest.cpp
@@ -15,8 +15,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/IK/JointLimitsTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/IK/tests/JointTrackingTaskTest.cpp b/src/IK/tests/JointTrackingTaskTest.cpp
index bfd1017440..13bafa8ce3 100644
--- a/src/IK/tests/JointTrackingTaskTest.cpp
+++ b/src/IK/tests/JointTrackingTaskTest.cpp
@@ -13,8 +13,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/IK/JointTrackingTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/IK/tests/QPFixedBaseInverseKinematicsTest.cpp b/src/IK/tests/QPFixedBaseInverseKinematicsTest.cpp
index b216ab9fa7..a213b9ea6a 100644
--- a/src/IK/tests/QPFixedBaseInverseKinematicsTest.cpp
+++ b/src/IK/tests/QPFixedBaseInverseKinematicsTest.cpp
@@ -9,7 +9,7 @@
 #include <catch2/catch_test_macros.hpp>
 
 // std
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/Transform.h>
 #include <memory>
 #include <random>
 
@@ -28,8 +28,8 @@
 #include <BipedalLocomotion/ContinuousDynamicalSystem/FloatingBaseSystemKinematics.h>
 #include <BipedalLocomotion/ContinuousDynamicalSystem/ForwardEuler.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/QPInverseKinematicsTest.cpp b/src/IK/tests/QPInverseKinematicsTest.cpp
index 87f757859c..17273df3d0 100644
--- a/src/IK/tests/QPInverseKinematicsTest.cpp
+++ b/src/IK/tests/QPInverseKinematicsTest.cpp
@@ -33,8 +33,8 @@
 #include <BipedalLocomotion/ContinuousDynamicalSystem/FloatingBaseSystemKinematics.h>
 #include <BipedalLocomotion/ContinuousDynamicalSystem/ForwardEuler.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/R3TaskTest.cpp b/src/IK/tests/R3TaskTest.cpp
index f88692c106..fae6196db3 100644
--- a/src/IK/tests/R3TaskTest.cpp
+++ b/src/IK/tests/R3TaskTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/IK/R3Task.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/SE3TaskTest.cpp b/src/IK/tests/SE3TaskTest.cpp
index 8758077703..5d2c7e0bab 100644
--- a/src/IK/tests/SE3TaskTest.cpp
+++ b/src/IK/tests/SE3TaskTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/IK/SE3Task.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/IK/tests/SO3TaskTest.cpp b/src/IK/tests/SO3TaskTest.cpp
index 485dd5fa4f..7fd448c2ed 100644
--- a/src/IK/tests/SO3TaskTest.cpp
+++ b/src/IK/tests/SO3TaskTest.cpp
@@ -15,8 +15,8 @@
 
 #include <BipedalLocomotion/IK/SO3Task.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/ML/src/MANNAutoregressive.cpp b/src/ML/src/MANNAutoregressive.cpp
index 14e083bb03..99f48ad5aa 100644
--- a/src/ML/src/MANNAutoregressive.cpp
+++ b/src/ML/src/MANNAutoregressive.cpp
@@ -16,7 +16,7 @@
 #include <BipedalLocomotion/Math/Constants.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 #include <manif/SE3.h>
 
 using namespace BipedalLocomotion::ML;
diff --git a/src/ML/src/MANNTrajectoryGenerator.cpp b/src/ML/src/MANNTrajectoryGenerator.cpp
index 7d5fd5b0a4..b825466023 100644
--- a/src/ML/src/MANNTrajectoryGenerator.cpp
+++ b/src/ML/src/MANNTrajectoryGenerator.cpp
@@ -12,10 +12,10 @@
 #include <BipedalLocomotion/ML/MANNTrajectoryGenerator.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/Model.h>
 #include <manif/SE3.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 using namespace BipedalLocomotion::ML;
 using namespace BipedalLocomotion;
diff --git a/src/ML/tests/MANNTrajectoryGeneratorTest.cpp b/src/ML/tests/MANNTrajectoryGeneratorTest.cpp
index 8334d3fdda..1c3aa494d8 100644
--- a/src/ML/tests/MANNTrajectoryGeneratorTest.cpp
+++ b/src/ML/tests/MANNTrajectoryGeneratorTest.cpp
@@ -7,8 +7,8 @@
 
 #include <memory>
 
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/ModelLoader.h>
 
 // Catch2
 #include <catch2/catch_test_macros.hpp>
diff --git a/src/Planners/src/UnicyclePlanner.cpp b/src/Planners/src/UnicyclePlanner.cpp
index 9db4902d06..e3b0ad0709 100644
--- a/src/Planners/src/UnicyclePlanner.cpp
+++ b/src/Planners/src/UnicyclePlanner.cpp
@@ -12,8 +12,8 @@
 #include <UnicycleGenerator.h>
 #include <UnicyclePlanner.h>
 #include <chrono>
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/VectorFixSize.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/VectorFixSize.h>
 #include <manif/SE3.h>
 
 #include <cassert>
diff --git a/src/System/include/BipedalLocomotion/System/LinearTask.h b/src/System/include/BipedalLocomotion/System/LinearTask.h
index 0bf854cd5c..05b9d88bc7 100644
--- a/src/System/include/BipedalLocomotion/System/LinearTask.h
+++ b/src/System/include/BipedalLocomotion/System/LinearTask.h
@@ -13,7 +13,7 @@
 
 #include <Eigen/Dense>
 
-#include <iDynTree/Core/MatrixView.h>
+#include <iDynTree/MatrixView.h>
 
 #include <BipedalLocomotion/ParametersHandler/IParametersHandler.h>
 #include <BipedalLocomotion/System/VariablesHandler.h>
diff --git a/src/TSID/src/AngularMomentumTask.cpp b/src/TSID/src/AngularMomentumTask.cpp
index ac7bbc20d5..14f5d7a7ac 100644
--- a/src/TSID/src/AngularMomentumTask.cpp
+++ b/src/TSID/src/AngularMomentumTask.cpp
@@ -8,8 +8,8 @@
 #include <BipedalLocomotion/TSID/AngularMomentumTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/BaseDynamicsTask.cpp b/src/TSID/src/BaseDynamicsTask.cpp
index cd2e304dc4..8fbc060bb8 100644
--- a/src/TSID/src/BaseDynamicsTask.cpp
+++ b/src/TSID/src/BaseDynamicsTask.cpp
@@ -8,8 +8,8 @@
 #include <BipedalLocomotion/TSID/BaseDynamicsTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/CoMTask.cpp b/src/TSID/src/CoMTask.cpp
index 69a4f1980a..20775bb7f0 100644
--- a/src/TSID/src/CoMTask.cpp
+++ b/src/TSID/src/CoMTask.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/TSID/CoMTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/FeasibleContactWrenchTask.cpp b/src/TSID/src/FeasibleContactWrenchTask.cpp
index 9c47dd42cb..3fe9a16bf6 100644
--- a/src/TSID/src/FeasibleContactWrenchTask.cpp
+++ b/src/TSID/src/FeasibleContactWrenchTask.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/TSID/FeasibleContactWrenchTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::TSID;
diff --git a/src/TSID/src/JointDynamicsTask.cpp b/src/TSID/src/JointDynamicsTask.cpp
index d83c9f19ed..e230d9d2b2 100644
--- a/src/TSID/src/JointDynamicsTask.cpp
+++ b/src/TSID/src/JointDynamicsTask.cpp
@@ -8,8 +8,8 @@
 #include <BipedalLocomotion/TSID/JointDynamicsTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/JointTrackingTask.cpp b/src/TSID/src/JointTrackingTask.cpp
index c458fda959..52e2c78e80 100644
--- a/src/TSID/src/JointTrackingTask.cpp
+++ b/src/TSID/src/JointTrackingTask.cpp
@@ -8,7 +8,7 @@
 #include <BipedalLocomotion/TSID/JointTrackingTask.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::TSID;
diff --git a/src/TSID/src/R3Task.cpp b/src/TSID/src/R3Task.cpp
index a38e65f307..4958349674 100644
--- a/src/TSID/src/R3Task.cpp
+++ b/src/TSID/src/R3Task.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/TSID/R3Task.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/SE3Task.cpp b/src/TSID/src/SE3Task.cpp
index d679eec38d..a99816b768 100644
--- a/src/TSID/src/SE3Task.cpp
+++ b/src/TSID/src/SE3Task.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/TSID/SE3Task.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/SO3Task.cpp b/src/TSID/src/SO3Task.cpp
index 8c7ffd42df..5e5fa43056 100644
--- a/src/TSID/src/SO3Task.cpp
+++ b/src/TSID/src/SO3Task.cpp
@@ -9,8 +9,8 @@
 #include <BipedalLocomotion/TSID/SO3Task.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/Model.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/Model.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/src/VariableRegularizationTask.cpp b/src/TSID/src/VariableRegularizationTask.cpp
index 313243effa..058f670521 100644
--- a/src/TSID/src/VariableRegularizationTask.cpp
+++ b/src/TSID/src/VariableRegularizationTask.cpp
@@ -9,7 +9,7 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/TextLogging/Logger.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
+#include <iDynTree/EigenHelpers.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::TSID;
diff --git a/src/TSID/tests/AngularMomentumTaskTest.cpp b/src/TSID/tests/AngularMomentumTaskTest.cpp
index fd05a2f3cd..bbda9bd05f 100644
--- a/src/TSID/tests/AngularMomentumTaskTest.cpp
+++ b/src/TSID/tests/AngularMomentumTaskTest.cpp
@@ -13,8 +13,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/TSID/AngularMomentumTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/TSID/tests/CoMTaskTest.cpp b/src/TSID/tests/CoMTaskTest.cpp
index bd012472cc..2229b131e1 100644
--- a/src/TSID/tests/CoMTaskTest.cpp
+++ b/src/TSID/tests/CoMTaskTest.cpp
@@ -15,8 +15,8 @@
 
 #include <LieGroupControllers/ProportionalDerivativeController.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/tests/DynamicsTaskTest.cpp b/src/TSID/tests/DynamicsTaskTest.cpp
index 6e272f5f2a..2e7f734e38 100644
--- a/src/TSID/tests/DynamicsTaskTest.cpp
+++ b/src/TSID/tests/DynamicsTaskTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/TSID/BaseDynamicsTask.h>
 #include <BipedalLocomotion/TSID/JointDynamicsTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/TSID/tests/FeasibleContactWrenchTaskTest.cpp b/src/TSID/tests/FeasibleContactWrenchTaskTest.cpp
index b5b6c48bac..fedb6f2584 100644
--- a/src/TSID/tests/FeasibleContactWrenchTaskTest.cpp
+++ b/src/TSID/tests/FeasibleContactWrenchTaskTest.cpp
@@ -15,8 +15,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/TSID/FeasibleContactWrenchTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/TSID/tests/JointTrackingTaskTest.cpp b/src/TSID/tests/JointTrackingTaskTest.cpp
index 713ea3da64..4c6101fb84 100644
--- a/src/TSID/tests/JointTrackingTaskTest.cpp
+++ b/src/TSID/tests/JointTrackingTaskTest.cpp
@@ -13,8 +13,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/TSID/JointTrackingTask.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 #include <Eigen/Dense>
 
diff --git a/src/TSID/tests/QPFixedBaseTSIDTest.cpp b/src/TSID/tests/QPFixedBaseTSIDTest.cpp
index 64c6e64b88..dacf56a275 100644
--- a/src/TSID/tests/QPFixedBaseTSIDTest.cpp
+++ b/src/TSID/tests/QPFixedBaseTSIDTest.cpp
@@ -24,8 +24,8 @@
 #include <BipedalLocomotion/TSID/QPFixedBaseTSID.h>
 #include <BipedalLocomotion/TSID/SE3Task.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/tests/R3TaskTest.cpp b/src/TSID/tests/R3TaskTest.cpp
index fd407393a0..85f4c988af 100644
--- a/src/TSID/tests/R3TaskTest.cpp
+++ b/src/TSID/tests/R3TaskTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/ParametersHandler/StdImplementation.h>
 #include <BipedalLocomotion/System/VariablesHandler.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/tests/SE3TaskTest.cpp b/src/TSID/tests/SE3TaskTest.cpp
index ae63e63c7f..c4eb7bf5a3 100644
--- a/src/TSID/tests/SE3TaskTest.cpp
+++ b/src/TSID/tests/SE3TaskTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/TSID/SE3Task.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/TSID/tests/SO3TaskTest.cpp b/src/TSID/tests/SO3TaskTest.cpp
index 6265a94a80..e10a0d97bb 100644
--- a/src/TSID/tests/SO3TaskTest.cpp
+++ b/src/TSID/tests/SO3TaskTest.cpp
@@ -14,8 +14,8 @@
 #include <BipedalLocomotion/System/VariablesHandler.h>
 #include <BipedalLocomotion/TSID/SO3Task.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Model/ModelTestUtils.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/ModelTestUtils.h>
 
 using namespace BipedalLocomotion::ParametersHandler;
 using namespace BipedalLocomotion::System;
diff --git a/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/Helper.h b/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/Helper.h
index 345657dd53..8bda9bc42a 100644
--- a/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/Helper.h
+++ b/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/Helper.h
@@ -18,7 +18,7 @@
 #include <yarp/os/Value.h>
 #include <yarp/sig/Vector.h>
 
-#include <iDynTree/Core/VectorDynSize.h>
+#include <iDynTree/VectorDynSize.h>
 
 namespace BipedalLocomotion
 {
diff --git a/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionClient.h b/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionClient.h
index 31c5f5c54a..7496e2d730 100644
--- a/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionClient.h
+++ b/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionClient.h
@@ -15,7 +15,7 @@
 #include <BipedalLocomotion/YarpUtilities/VectorsCollection.h>
 #include <BipedalLocomotion/YarpUtilities/VectorsCollectionMetadata.h>
 
-#include <iDynTree/Core/Span.h>
+#include <iDynTree/Span.h>
 
 namespace BipedalLocomotion
 {
diff --git a/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionServer.h b/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionServer.h
index 8bff73f642..01bb12a172 100644
--- a/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionServer.h
+++ b/src/YarpUtilities/include/BipedalLocomotion/YarpUtilities/VectorsCollectionServer.h
@@ -16,7 +16,7 @@
 #include <BipedalLocomotion/YarpUtilities/VectorsCollectionMetadata.h>
 #include <BipedalLocomotion/YarpUtilities/VectorsCollectionMetadataService.h>
 
-#include <iDynTree/Core/Span.h>
+#include <iDynTree/Span.h>
 
 namespace BipedalLocomotion
 {
diff --git a/utilities/mas-imu-test/include/BipedalLocomotion/MasImuTest.h b/utilities/mas-imu-test/include/BipedalLocomotion/MasImuTest.h
index 1f68b53520..9783e24f0d 100644
--- a/utilities/mas-imu-test/include/BipedalLocomotion/MasImuTest.h
+++ b/utilities/mas-imu-test/include/BipedalLocomotion/MasImuTest.h
@@ -21,12 +21,12 @@
 #include <yarp/dev/IEncodersTimed.h>
 
 // iDynTree
-#include <iDynTree/Model/Model.h>
-#include <iDynTree/Model/Traversal.h>
-#include <iDynTree/Core/Rotation.h>
+#include <iDynTree/Model.h>
+#include <iDynTree/Traversal.h>
+#include <iDynTree/Rotation.h>
 #include <iDynTree/KinDynComputations.h>
-#include <iDynTree/Core/VectorDynSize.h>
-#include <iDynTree/Core/Transform.h>
+#include <iDynTree/VectorDynSize.h>
+#include <iDynTree/Transform.h>
 
 // Eigen
 #include <Eigen/Core>
diff --git a/utilities/mas-imu-test/src/MasImuTest.cpp b/utilities/mas-imu-test/src/MasImuTest.cpp
index a9861be091..2b8fdbad52 100644
--- a/utilities/mas-imu-test/src/MasImuTest.cpp
+++ b/utilities/mas-imu-test/src/MasImuTest.cpp
@@ -10,11 +10,11 @@
 #include <BipedalLocomotion/Math/Constants.h>
 #include <BipedalLocomotion/YarpUtilities/Helper.h>
 
-#include <iDynTree/Core/EigenHelpers.h>
-#include <iDynTree/Core/SO3Utils.h>
-#include <iDynTree/Model/IJoint.h>
-#include <iDynTree/ModelIO/ModelLoader.h>
-#include <iDynTree/yarp/YARPConfigurationsLoader.h>
+#include <iDynTree/EigenHelpers.h>
+#include <iDynTree/SO3Utils.h>
+#include <iDynTree/IJoint.h>
+#include <iDynTree/ModelLoader.h>
+#include <iDynTree/YARPConfigurationsLoader.h>
 
 #include <yarp/os/LogStream.h>