diff --git a/common.mk b/common.mk
index c15380f8..1a8f9b83 100644
--- a/common.mk
+++ b/common.mk
@@ -218,6 +218,15 @@ $(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST) $(ALL_MODS_FILELIST) $(BB_MODS_FILEL
 	$(SED) -i 's/\.\///' $(BB_MODS_FILELIST)
 	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_MODEL_HRCHY_JSON) $(TOP_MODS_FILELIST) $(MODEL_MODS_FILELIST)
+	$(base_dir)/scripts/split-bb-files.py \
+		--in-top-f $(TOP_MODS_FILELIST) \
+		--in-model-f $(MODEL_MODS_FILELIST) \
+		--in-top-hrchy-json $(MFC_MODEL_HRCHY_JSON) \
+		--in-bb-f $(BB_MODS_FILELIST) \
+		--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)
 	$(base_dir)/scripts/split-mems-conf.py \
 		--in-smems-conf $(MFC_SMEMS_CONF) \
@@ -239,7 +248,7 @@ $(MODEL_SMEMS_FILE) $(MODEL_SMEMS_FIR) &: $(MODEL_SMEMS_CONF) | $(TOP_SMEMS_FILE
 ########################################################################################
 # remove duplicate files and headers in list of simulation file inputs
 ########################################################################################
-$(sim_common_files): $(sim_files) $(ALL_MODS_FILELIST) $(TOP_SMEMS_FILE) $(MODEL_SMEMS_FILE)
+$(sim_common_files): $(sim_files) $(ALL_MODS_FILELIST) $(TOP_SMEMS_FILE) $(MODEL_SMEMS_FILE) $(TOP_BB_MODS_FILELIST) $(MODEL_BB_MODS_FILELIST)
 	sort -u $(sim_files) $(ALL_MODS_FILELIST) | grep -v '.*\.\(svh\|h\)$$' > $@
 	echo "$(TOP_SMEMS_FILE)" >> $@
 	echo "$(MODEL_SMEMS_FILE)" >> $@
diff --git a/scripts/split-bb-files.py b/scripts/split-bb-files.py
new file mode 100755
index 00000000..257001c7
--- /dev/null
+++ b/scripts/split-bb-files.py
@@ -0,0 +1,132 @@
+#!/usr/bin/env python3
+
+import os
+import json
+import argparse
+import sys
+from pathlib import Path
+from typing import List, Optional
+
+# Schema of *.f emitted by circt
+"""
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/SimUART.cc
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncQueueSource.sv
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncQueueSink.sv
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncQueueSource_1.sv
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncQueueSink_1.sv
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncQueueSource_2.sv
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncQueueSink_2.sv
+/scratch/joonho.whangbo/coding/chipyard/vlsi/generated-src/chipyard.TestHarness.RocketConfig/gen-collateral/AsyncResetSynchronizerShiftReg_w4_d3_i0.sv
+"""
+
+def bfs_collect_submodules(tree):
+  output = set()
+  q = [(tree['instance_name'], tree['module_name'], tree['instances'])]
+
+  while len(q) != 0:
+    front = q[0]
+    q.pop(0)
+
+    (inst, mod, child) = front
+    output.add(mod)
+    for c in child:
+      q.append((c['instance_name'], c['module_name'], c['instances']))
+  return output
+
+def get_modules(f):
+  lines = f.readlines()
+  module_list = list()
+  for line in lines:
+    try:
+      module_list.append(os.path.basename(line))
+    except:
+      print("Excepted a linux path, got something else")
+  return module_list
+
+def get_inner_modules(f):
+  lines = f.readlines()
+  inner_module_list = list()
+  for line in lines:
+    words = line.split()
+    if len(words) >= 2 and "module" == words[0]:
+      inner_module_list.append(words[1].replace("(", ""))
+  return inner_module_list
+
+def write_lines_to_file(lines, file_path):
+  with open(file_path, "w") as fp:
+    for line in lines:
+      fp.write("%s" % line)
+
+
+if __name__ == "__main__":
+  parser = argparse.ArgumentParser(description='Use *.model.f and *.top.f to restore the MODEL/TOP blackbox separation')
+  parser.add_argument('--in-top-f', type=str, required=True, help='List of generated files specific for TOP(DUT)')
+  parser.add_argument('--in-model-f', type=str, required=True, help='List of generated files specific for MODEL')
+  parser.add_argument('--in-bb-f', type=str, required=True, help='List of generated files specific for MODEL')
+  parser.add_argument('--in-top-hrchy-json', type=str, required=True, help='List containing hierarchy of top modules (top-module-hierarchy.json)')
+  parser.add_argument('--out-top-bb-f', type=str, required=True, help='List of blackbox modules for TOP')
+  parser.add_argument('--out-model-bb-f', type=str, required=True, help='List of blackbox modules for MODEL')
+  args = parser.parse_args()
+
+  itf = open(args.in_top_f)
+  top_modules = set(get_modules(itf))
+  itf.close()
+
+  imf = open(args.in_model_f)
+  model_modules = set(get_modules(imf))
+  imf.close()
+
+  ihj = open(args.in_top_hrchy_json)
+  ihj_data = json.load(ihj)
+  top_inner_modules = bfs_collect_submodules(ihj_data)
+  ihj.close()
+
+  ibf = open(args.in_bb_f)
+  lines = ibf.readlines()
+
+  """
+  " model  top
+  " o      o   -> model
+  " x      o   -> top
+  " x      x   -> model
+  "  - check inner module
+  "  - currently, there is no way of knowing if certain inner modules(actual verilog
+  "  modules inside the files are all included in TOP or MODEL)
+  "  - for now, assume that if a innter module is included in TOP, the file itself
+  "  is also for TOP
+  """
+  tbf = list()
+  mbf = list()
+  unknown = list()
+  for line in lines:
+    module = os.path.basename(line)
+    extension = os.path.splitext(module)[1]
+    if module in model_modules:
+      mbf.append(line)
+    elif module in top_modules:
+      tbf.append(line)
+    elif ".v" not in extension and ".sv" not in extension:
+      mbf.append(line)
+    else:
+      unknown.append(line)
+
+
+  for line in unknown:
+    f = open(Path(line.replace("\n", "")))
+    inner_modules = get_inner_modules(f)
+    f.close()
+
+    inner_module_in_top = False
+    for im in inner_modules:
+      if im in top_inner_modules:
+        inner_module_in_top = True
+        break
+    if inner_module_in_top:
+      tbf.append(line)
+    else:
+      mbf.append(line)
+
+  write_lines_to_file(tbf, args.out_top_bb_f)
+  write_lines_to_file(mbf, args.out_model_bb_f)
+
+  ibf.close()
diff --git a/variables.mk b/variables.mk
index fab54a6a..c0655fab 100644
--- a/variables.mk
+++ b/variables.mk
@@ -182,6 +182,8 @@ MODEL_MODS_FILELIST ?= $(build_dir)/$(long_name).model.f
 # list of all blackbox files (may be included in the top/model.f files)
 # this has the build_dir appended
 BB_MODS_FILELIST ?= $(build_dir)/$(long_name).bb.f
+TOP_BB_MODS_FILELIST ?= $(build_dir)/$(long_name).top.bb.f
+MODEL_BB_MODS_FILELIST ?= $(build_dir)/$(long_name).model.bb.f
 # all module files to include (top, model, bb included)
 ALL_MODS_FILELIST ?= $(build_dir)/$(long_name).all.f
 
diff --git a/vlsi/Makefile b/vlsi/Makefile
index 452c64ef..3cd4577d 100644
--- a/vlsi/Makefile
+++ b/vlsi/Makefile
@@ -61,7 +61,7 @@ ifneq ($(CUSTOM_VLOG), )
 else
 	VLSI_RTL = $(shell cat $(TOP_MODS_FILELIST)) $(TOP_SMEMS_FILE) 
 	# TODO: have MFC split top & harness blackboxes
-	VLSI_BB = $(build_dir)/EICG_wrapper.v $(shell rev $(BB_MODS_FILELIST) | sed -E 's/cc(.*)/c\1/g' | uniq -s 1 | sed '/c\./d' | rev)
+	VLSI_BB = $(build_dir)/EICG_wrapper.v $(TOP_BB_MODS_FILELIST)
 endif
 
 .PHONY: default