diff --git a/dv/uvm/core_ibex/Makefile b/dv/uvm/core_ibex/Makefile
index 46b18e33..12ea81c9 100644
--- a/dv/uvm/core_ibex/Makefile
+++ b/dv/uvm/core_ibex/Makefile
@@ -236,8 +236,6 @@ tests-and-seeds := \
             --iterations $(ITERATIONS) \
             --ibex-config $(IBEX_CONFIG))
 
-REGEX_EMPTY_LINES := '/^$$/d'
-
 ###############################################################################
 ###############################################################################
 # Build the Random Instruction Generator
@@ -326,7 +324,6 @@ $(metadata)/.instr_gen.run.stamp: \
 	                   +pmp_granularity=${PMP_GRANULARITY} +tvec_alignment=8" \
 	       --debug $(INSTR_GEN_RUN_COMMANDS) # Write all the commands to execute into here...
 	@ # Construct the sub-makefile from the commands, then call it
-	@sed -i $(REGEX_EMPTY_LINES) $(INSTR_GEN_RUN_COMMANDS)
 	$(verb)./scripts/construct_makefile.py \
 	         --output=$(OUT-SEED)/instr_gen/run.mk \
 	         --test_cmds=$(INSTR_GEN_RUN_COMMANDS) \
@@ -383,7 +380,6 @@ $(metadata)/.iss.run.stamp: \
 	       ${_RISCV_DV_OPTS} \
 	       --debug $(ISS_COMMANDS) # Write all the commands to execute into here...
 	@ # Construct the sub-makefile from the commands, then call it
-	@sed -i $(REGEX_EMPTY_LINES) $(ISS_COMMANDS)
 	$(verb)./scripts/construct_makefile.py \
 	         --output=$(OUT-SEED)/instr_gen/iss.mk \
 	         --test_cmds=$(ISS_COMMANDS)
diff --git a/dv/uvm/core_ibex/scripts/construct_makefile.py b/dv/uvm/core_ibex/scripts/construct_makefile.py
index d2b6ec4e..5bb94c51 100755
--- a/dv/uvm/core_ibex/scripts/construct_makefile.py
+++ b/dv/uvm/core_ibex/scripts/construct_makefile.py
@@ -19,10 +19,17 @@ def transform(discard_stdstreams: bool,
 
     with open(cmdlist_path) as f, \
          open(makefile_path, 'w', encoding='UTF-8') as outfile:
-        for i, line in enumerate(f):
-            outfile.write(f'{i}:\n')
+        ctr = 0
+        for line in f:
+            line = line.strip()
+            if not line:
+                continue
+
+            outfile.write(f'{ctr}:\n')
             outfile.write('\t' + line.strip() + tail)
-        outfile.write(f'CMDS := $(shell seq 0 {i})\n')
+            ctr += 1
+
+        outfile.write(f'CMDS := $(shell seq 0 {ctr - 1})\n')
         outfile.write('all: $(CMDS)')