diff --git a/src/main/java/org/checkerframework/specimin/SpeciminRunner.java b/src/main/java/org/checkerframework/specimin/SpeciminRunner.java
index 3b14f32b..9062c68d 100644
--- a/src/main/java/org/checkerframework/specimin/SpeciminRunner.java
+++ b/src/main/java/org/checkerframework/specimin/SpeciminRunner.java
@@ -5,7 +5,6 @@
 import com.github.javaparser.ast.Node;
 import com.github.javaparser.ast.PackageDeclaration;
 import com.github.javaparser.ast.body.ClassOrInterfaceDeclaration;
-import com.github.javaparser.printer.lexicalpreservation.LexicalPreservingPrinter;
 import com.github.javaparser.symbolsolver.JavaSymbolSolver;
 import com.github.javaparser.symbolsolver.model.resolution.TypeSolver;
 import com.github.javaparser.symbolsolver.resolution.typesolvers.CombinedTypeSolver;
@@ -14,7 +13,7 @@
 import com.github.javaparser.symbolsolver.resolution.typesolvers.ReflectionTypeSolver;
 import java.io.File;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
+import java.io.PrintWriter;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Collection;
@@ -175,9 +174,6 @@ public static void performMinimization(
         new MethodPrunerVisitor(finder.getTargetMethods(), finder.getUsedMembers());
 
     for (CompilationUnit cu : parsedTargetFiles.values()) {
-      // This must happen before any modifications to each compilation unit, or
-      // the printer won't know about them. (It registers an observer.)
-      LexicalPreservingPrinter.setup(cu);
       cu.accept(methodPruner, null);
     }
     for (Entry<String, CompilationUnit> target : parsedTargetFiles.entrySet()) {
@@ -191,7 +187,6 @@ public static void performMinimization(
           continue;
         }
       }
-
       Path targetOutputPath = Path.of(outputDirectory, target.getKey());
       // Create any parts of the directory structure that don't already exist.
       Path dirContainingOutputFile = targetOutputPath.getParent();
@@ -201,10 +196,11 @@ public static void performMinimization(
       if (dirContainingOutputFile != null) {
         Files.createDirectories(dirContainingOutputFile);
       }
+      // Write the string representation of CompilationUnit to the file
       try {
-        Files.write(
-            targetOutputPath,
-            LexicalPreservingPrinter.print(target.getValue()).getBytes(StandardCharsets.UTF_8));
+        PrintWriter writer = new PrintWriter(targetOutputPath.toFile());
+        writer.print(target.getValue());
+        writer.close();
       } catch (IOException e) {
         System.out.println("failed to write output file " + targetOutputPath);
         System.out.println("with error: " + e);
diff --git a/src/test/java/org/checkerframework/specimin/RemovingCommentsTest.java b/src/test/java/org/checkerframework/specimin/RemovingCommentsTest.java
new file mode 100644
index 00000000..af9287d9
--- /dev/null
+++ b/src/test/java/org/checkerframework/specimin/RemovingCommentsTest.java
@@ -0,0 +1,15 @@
+package org.checkerframework.specimin;
+
+import java.io.IOException;
+import org.junit.Test;
+
+/** This test checks that if Specimin will remove comments from the input code */
+public class RemovingCommentsTest {
+  @Test
+  public void runTest() throws IOException {
+    SpeciminTestExecutor.runTestWithoutJarPaths(
+        "removingcomments",
+        new String[] {"com/example/Simple.java"},
+        new String[] {"com.example.Simple#test()"});
+  }
+}
diff --git a/src/test/java/org/checkerframework/specimin/SpeciminTestExecutor.java b/src/test/java/org/checkerframework/specimin/SpeciminTestExecutor.java
index 7df76b8a..e7a0c48d 100644
--- a/src/test/java/org/checkerframework/specimin/SpeciminTestExecutor.java
+++ b/src/test/java/org/checkerframework/specimin/SpeciminTestExecutor.java
@@ -90,6 +90,8 @@ public static void runTest(
       builder.command(
           "diff",
           "-qr",
+          "-w",
+          "-B",
           outputDir.toAbsolutePath().toString(),
           Path.of("src/test/resources/" + testName + "/expected").toAbsolutePath().toString());
     }
diff --git a/src/test/resources/innerclass/expected/com/example/Maternal.java b/src/test/resources/innerclass/expected/com/example/Maternal.java
index 21d76a34..62d581f4 100644
--- a/src/test/resources/innerclass/expected/com/example/Maternal.java
+++ b/src/test/resources/innerclass/expected/com/example/Maternal.java
@@ -1,4 +1,6 @@
 package com.example;
+
 public class Maternal {
+
     public String maternalLastName = null;
 }
diff --git a/src/test/resources/innerclass/expected/com/example/OuterFamily.java b/src/test/resources/innerclass/expected/com/example/OuterFamily.java
index 4a3e235d..5fa89315 100644
--- a/src/test/resources/innerclass/expected/com/example/OuterFamily.java
+++ b/src/test/resources/innerclass/expected/com/example/OuterFamily.java
@@ -1,13 +1,15 @@
 package com.example;
 
 class OuterFamily extends Maternal {
+
     class InnerFamily extends Paternal {
+
         public String getLastName() {
             return paternalLastName;
         }
     }
-    // point A
+
     public String getLastName() {
         return maternalLastName;
     }
-}
\ No newline at end of file
+}
diff --git a/src/test/resources/innerclass/expected/com/example/Paternal.java b/src/test/resources/innerclass/expected/com/example/Paternal.java
index 985bb5c1..b1ac0153 100644
--- a/src/test/resources/innerclass/expected/com/example/Paternal.java
+++ b/src/test/resources/innerclass/expected/com/example/Paternal.java
@@ -1,4 +1,6 @@
 package com.example;
+
 public class Paternal {
+
     public String paternalLastName = null;
 }
diff --git a/src/test/resources/jarfile/expected/an/old/library/Book.java b/src/test/resources/jarfile/expected/an/old/library/Book.java
index f8254949..8a4c1adb 100644
--- a/src/test/resources/jarfile/expected/an/old/library/Book.java
+++ b/src/test/resources/jarfile/expected/an/old/library/Book.java
@@ -1,4 +1,5 @@
 package an.old.library;
+
 public class Book {
 
     public Book(int parameter0) {
diff --git a/src/test/resources/jarfile/expected/com/example/Simple.java b/src/test/resources/jarfile/expected/com/example/Simple.java
index aa145f6f..ce9c6987 100644
--- a/src/test/resources/jarfile/expected/com/example/Simple.java
+++ b/src/test/resources/jarfile/expected/com/example/Simple.java
@@ -3,7 +3,7 @@
 import an.old.library.Book;
 
 class Simple {
-    // Target method.
+
     int test() {
         Book bookOfTheYear = new Book(2023);
         return bookOfTheYear.getRates().length();
diff --git a/src/test/resources/onefilesimple/expected/com/example/Simple.java b/src/test/resources/onefilesimple/expected/com/example/Simple.java
index c60b702e..3a35e628 100644
--- a/src/test/resources/onefilesimple/expected/com/example/Simple.java
+++ b/src/test/resources/onefilesimple/expected/com/example/Simple.java
@@ -1,7 +1,7 @@
 package com.example;
 
 class Simple {
-    // Target method.
+
     void bar() {
         Object obj = new Object();
         obj = baz(obj);
diff --git a/src/test/resources/removingcomments/expected/com/example/Simple.java b/src/test/resources/removingcomments/expected/com/example/Simple.java
new file mode 100644
index 00000000..6597d67f
--- /dev/null
+++ b/src/test/resources/removingcomments/expected/com/example/Simple.java
@@ -0,0 +1,13 @@
+package com.example;
+
+class Simple {
+
+    static int returnTen() {
+        throw new Error();
+    }
+
+    static void test() {
+        int y = returnTen();
+        Simple s = new Simple();
+    }
+}
diff --git a/src/test/resources/removingcomments/input/com/example/Simple.java b/src/test/resources/removingcomments/input/com/example/Simple.java
new file mode 100644
index 00000000..64708522
--- /dev/null
+++ b/src/test/resources/removingcomments/input/com/example/Simple.java
@@ -0,0 +1,19 @@
+package com.example;
+
+class Simple {
+    static int returnFive() {
+        return 5;
+    }
+    static int returnTen() {
+        return returnFive() * 2;
+    }
+
+    /**
+     * This method is used to test if the comments (including Javadoc) are all removed by Specimin
+     */
+    static void test() {
+        // the comment here should be removed
+        int y = returnTen();
+        Simple s = new Simple();
+    }
+}