diff --git a/common.mk b/common.mk
index a4668075dc..5c1f2461d1 100644
--- a/common.mk
+++ b/common.mk
@@ -231,7 +231,7 @@ $(SFC_MFC_TARGETS) &: $(FIRRTL_FILE) $(FINAL_ANNO_FILE) $(SFC_LEVEL) $(EXTRA_FIR
 	$(SED) -i 's/.*/& /' $(MFC_SMEMS_CONF) # need trailing space for SFC macrocompiler
 # DOC include end: FirrtlCompiler
 
-$(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILELIST) &: $(MFC_MODEL_HRCHY_JSON) $(MFC_FILELIST) $(MFC_BB_MODS_FILELIST)
+$(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILELIST) $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) &: $(MFC_MODEL_HRCHY_JSON) $(MFC_FILELIST) $(MFC_BB_MODS_FILELIST)
 	$(base_dir)/scripts/split-module-files.py \
 		--model-hier-json $(MFC_MODEL_HRCHY_JSON) \
 		--dut $(TOP) \
@@ -243,6 +243,14 @@ $(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILEL
 	$(SED) -i 's/\.\///' $(TOP_MODS_FILELIST)
 	$(SED) -i 's/\.\///' $(MODEL_MODS_FILELIST)
 	$(SED) -i 's/\.\///' $(BB_MODS_FILELIST)
+	$(base_dir)/scripts/uniqify-module-names.py \
+		--top-filelist $(TOP_MODS_FILELIST) \
+		--mod-filelist $(MODEL_MODS_FILELIST) \
+		--gen-collateral-path $(GEN_COLLATERAL_DIR) \
+		--model-hier-json $(MFC_MODEL_HRCHY_JSON) \
+		--out-model-hier-json $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) \
+		--dut $(TOP) \
+		--model $(MODEL)
 	sort -u $(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(BB_MODS_FILELIST) > $(ALL_MODS_FILELIST)
 
 $(TOP_BB_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST) &: $(BB_MODS_FILELIST) $(MFC_TOP_HRCHY_JSON) $(FINAL_ANNO_FILE)
@@ -253,10 +261,10 @@ $(TOP_BB_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST) &: $(BB_MODS_FILELIST) $(MFC_T
 		--out-top-bb-f $(TOP_BB_MODS_FILELIST) \
 		--out-model-bb-f $(MODEL_BB_MODS_FILELIST)
 
-$(TOP_SMEMS_CONF) $(MODEL_SMEMS_CONF) &:  $(MFC_SMEMS_CONF) $(MFC_MODEL_HRCHY_JSON)
+$(TOP_SMEMS_CONF) $(MODEL_SMEMS_CONF) &:  $(MFC_SMEMS_CONF) $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED)
 	$(base_dir)/scripts/split-mems-conf.py \
 		--in-smems-conf $(MFC_SMEMS_CONF) \
-		--in-model-hrchy-json $(MFC_MODEL_HRCHY_JSON) \
+		--in-model-hrchy-json $(MFC_MODEL_HRCHY_JSON_UNIQUIFIED) \
 		--dut-module-name $(TOP) \
 		--model-module-name $(MODEL) \
 		--out-dut-smems-conf $(TOP_SMEMS_CONF) \
diff --git a/scripts/uniqify-module-names.py b/scripts/uniqify-module-names.py
new file mode 100755
index 0000000000..a6255a8c90
--- /dev/null
+++ b/scripts/uniqify-module-names.py
@@ -0,0 +1,100 @@
+#!/usr/bin/env python3
+
+import json
+import argparse
+import shutil
+import os
+import datetime
+
+
+parser = argparse.ArgumentParser(description="")
+parser.add_argument("--top-filelist", type=str, required=True, help="Abs path to <top>.<model>.top.f")
+parser.add_argument("--mod-filelist", type=str, required=True, help="Abs path to <top>.<model>.model.f")
+parser.add_argument("--gen-collateral-path", dest="gcpath", type=str, required=True, help="Abs path to the gen-collateral directory")
+parser.add_argument("--model-hier-json", type=str, required=True, help="Path to hierarchy JSON emitted by firtool. Must include DUT as a module.")
+parser.add_argument("--out-model-hier-json", type=str, required=True, help="Path to updated hierarchy JSON emitted by this script.")
+parser.add_argument("--dut", type=str, required=True, help="Name of the DUT module.")
+parser.add_argument("--model", type=str, required=True, help="Name of the Model module.")
+args = parser.parse_args()
+
+
+MODEL_SFX=args.model + "_UNIQUIFIED"
+
+def bash(cmd):
+  fail = os.system(cmd)
+  if fail:
+    print(f'[*] failed to execute {cmd}')
+    sys.exit(1)
+  else:
+    print(cmd)
+
+def get_filelist(filelist):
+  fnames = []
+  with open(filelist) as f:
+    lines = f.readlines()
+    for line in lines:
+      try:
+        fname = line.split("/")[-1].strip()
+        fnames.append(fname)
+      except:
+        print(f"Something is wrong about this line '{line}'")
+  return fnames
+
+def update_filelist(cur_file, new_file):
+  bash(f"echo \"{args.gcpath}/{new_file}\" >> {os.path.join(args.gcpath, args.mod_filelist)}")
+
+def generate_copy(c, sfx):
+  (cur_name, ext) = os.path.splitext(c)
+  new_name = cur_name + "_" + sfx
+  new_file = new_name + ext
+
+  cur_file = os.path.join(args.gcpath, c)
+  new_file = os.path.join(args.gcpath, new_file)
+
+  shutil.copy(cur_file, new_file)
+  bash(f"sed -i s/\"module {cur_name}\"/\"module {new_name}\"/ {new_file}")
+  return new_file
+
+def dfs_update_modules(tree, common_fnames, visited, top_fnames):
+  # List of direct submodules to update
+  childs_to_update = list()
+  for child in tree['instances']:
+    # We don't have to change stuff that are under the dut
+    if (child['module_name'] == args.dut) or (child['module_name'] in visited):
+      continue
+    if dfs_update_modules(child, common_fnames, visited, top_fnames):
+      childs_to_update.append(child['module_name'])
+      if (child['module_name'] + ".sv") in common_fnames:
+        child['module_name'] = child['module_name'] + "_" + MODEL_SFX
+
+  cur_module = tree['module_name']
+  cur_file = cur_module + ".sv"
+  new_file = None
+
+  # cur_file is in the common list, or is a ancestor of of them, generate a new file
+  if (cur_file in common_fnames) or len(childs_to_update) > 0:
+    new_file = generate_copy(cur_file, MODEL_SFX)
+    update_filelist(cur_file, os.path.basename(new_file))
+
+  for submodule_name in childs_to_update:
+    if (submodule_name + ".sv") in common_fnames:
+      bash(f"sed -i s/\"{submodule_name}\"/\"{submodule_name}_{MODEL_SFX}\"/ {new_file}")
+
+  visited.add(cur_module)
+  return (new_file is not None)
+
+def main():
+  top_fnames = set(get_filelist(args.top_filelist))
+  mod_fnames = set(get_filelist(args.mod_filelist))
+  common_fnames = top_fnames.intersection(mod_fnames)
+
+  with open(args.model_hier_json) as imhj:
+    imhj_data = json.load(imhj)
+
+    with open(args.out_model_hier_json, "w+") as out_file:
+      visited = set()
+      dfs_update_modules(imhj_data, common_fnames, visited, top_fnames)
+      json.dump(imhj_data, out_file, indent=2)
+
+if __name__ == "__main__":
+  main()
diff --git a/variables.mk b/variables.mk
index eb9620f25b..1f659ac7ca 100644
--- a/variables.mk
+++ b/variables.mk
@@ -162,6 +162,7 @@ SFC_ANNO_FILE ?= $(build_dir)/$(long_name).sfc.anno.json
 # firtool compiler outputs
 MFC_TOP_HRCHY_JSON ?= $(build_dir)/top_module_hierarchy.json
 MFC_MODEL_HRCHY_JSON ?= $(build_dir)/model_module_hierarchy.json
+MFC_MODEL_HRCHY_JSON_UNIQUIFIED ?= $(build_dir)/model_module_hierarchy.uniquified.json
 MFC_SMEMS_CONF ?= $(build_dir)/$(long_name).mems.conf
 # hardcoded firtool outputs
 MFC_FILELIST = $(GEN_COLLATERAL_DIR)/filelist.f
diff --git a/vlsi/sim.mk b/vlsi/sim.mk
index 1f5b530d3b..13a7fcc3e0 100644
--- a/vlsi/sim.mk
+++ b/vlsi/sim.mk
@@ -10,7 +10,7 @@ $(SIM_CONF): $(sim_common_files)
 	echo "  top_module: $(VLSI_TOP)" >> $@
 	echo "  tb_name: ''" >> $@  # don't specify -top
 	echo "  input_files:" >> $@
-	for x in $$(comm -23 <(cat $(MODEL_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST) | sort -u) <(sort $(VLSI_RTL))) $(MODEL_SMEMS_FILE) $(SIM_FILE_REQS); do \
+	for x in $$(cat $(MODEL_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST) | sort -u) $(MODEL_SMEMS_FILE) $(SIM_FILE_REQS); do \
 		echo '    - "'$$x'"' >> $@; \
 	done
 	echo "  input_files_meta: 'append'" >> $@