diff --git a/NiChart_DLMUSE/__main__.py b/NiChart_DLMUSE/__main__.py
index 5375377..a56d396 100644
--- a/NiChart_DLMUSE/__main__.py
+++ b/NiChart_DLMUSE/__main__.py
@@ -163,6 +163,7 @@ def main() -> None:
 
     merge_output_data(out_dir)
     remove_subfolders(in_data)
+    remove_subfolders(out_dir)
 
 
 if __name__ == "__main__":
diff --git a/NiChart_DLMUSE/utils.py b/NiChart_DLMUSE/utils.py
index a95ba3f..788afde 100644
--- a/NiChart_DLMUSE/utils.py
+++ b/NiChart_DLMUSE/utils.py
@@ -224,5 +224,3 @@ def merge_output_data(in_dir: str) -> None:
             f"mv {in_dir}/{dir}/temp_working_dir/s6_combined/* {in_dir}/results/s6_combined/"
         )
         os.system(f"mv {in_dir}/{dir}/*.nii.gz {in_dir}/results/")
-
-    os.system(f"rm -r {in_dir}/split_*")