diff --git a/ci/Jenkinsfile b/ci/Jenkinsfile
index 6a2e064be0..8b987a16fa 100644
--- a/ci/Jenkinsfile
+++ b/ci/Jenkinsfile
@@ -221,7 +221,11 @@ pipeline {
                                                 def yaml_case = readYaml file: "${CUSTOM_WORKSPACE}/gfs/ci/cases/pr/${caseName}.yaml.tmp"
                                                 def build_system = yaml_case.experiment.system
                                                 try {
+                                                    // Remove any data in that might still be in the DATAROOT directory from previous runs
+                                                    STMP=sh(script: "${HOMEgfs}/ci/scripts/utils/get_config_var.py STMP ${CUSTOM_WORKSPACE}/RUNTESTS/EXPDIR/${pslot}", returnStdout: true).trim()
+                                                    sh(script: "rm -Rf ${STMP}/RUNDIRS/${pslot}")
                                                     sh(script: "${HOMEgfs}/ci/scripts/run-check_ci.sh ${CUSTOM_WORKSPACE} ${pslot} ${build_system}")
+                                                    sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cleanup_experiment ${CUSTOM_WORKSPACE}/RUNTESTS/EXPDIR/${pslot}")
                                                 } catch (Exception error_experment) {
                                                     sh(script: "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh cancel_batch_jobs ${pslot}")
                                                     ws(CUSTOM_WORKSPACE) {
diff --git a/ci/scripts/check_ci.sh b/ci/scripts/check_ci.sh
index 825d8f5e8b..a89a661042 100755
--- a/ci/scripts/check_ci.sh
+++ b/ci/scripts/check_ci.sh
@@ -168,8 +168,7 @@ for pr in ${pr_list}; do
     fi
     if [[ "${rocoto_state}" == "DONE" ]]; then
       #Remove Experment cases that completed successfully
-      rm -Rf "${pslot_dir}"
-      rm -Rf "${pr_dir}/RUNTESTS/COMROOT/${pslot}"
+      "${HOMEgfs}/ci/scripts/utils/ci_utils_wrapper.sh" cleanup_experiment "${pslot_dir}"
       rm -f "${output_ci_single}"
       # echo "\`\`\`" > "${output_ci_single}"
       DATE=$(date +'%D %r')
diff --git a/ci/scripts/utils/ci_utils.sh b/ci/scripts/utils/ci_utils.sh
index 2a51467d38..64988986fe 100755
--- a/ci/scripts/utils/ci_utils.sh
+++ b/ci/scripts/utils/ci_utils.sh
@@ -137,7 +137,6 @@ function publish_logs() {
     local PR_header="$1"
     local dir_path="$2"
     local file="$3"
-
     local full_paths=""
     while IFS= read -r line; do
         full_path="${dir_path}/${line}"
@@ -155,3 +154,24 @@ function publish_logs() {
     fi
     echo "${URL}"
 }
+
+function cleanup_experiment() {
+
+    local EXPDIR="$1"
+    local pslot
+    local ARCDIR
+    local ATARDIR
+    local COMROOT
+
+    EXPDIR="$1"
+    pslot=$(basename "${EXPDIR}")
+
+    # Use the Python utility to get the required variables
+    read -r ARCDIR ATARDIR STMP COMROOT < <("${HOMEgfs}/ci/scripts/utils/get_config_var.py" ARCDIR ATARDIR STMP COMROOT "${EXPDIR}") || true
+
+    rm -Rf "${STMP}/RUNDIRS/${pslot}"
+    rm -Rf "${ARCDIR:?}"
+    rm -Rf "${ATARDIR:?}"
+    rm -Rf "${COMROOT:?}"
+    rm -Rf "${EXPDIR}"
+}
diff --git a/ci/scripts/utils/get_config_var.py b/ci/scripts/utils/get_config_var.py
new file mode 100755
index 0000000000..3e63fcf376
--- /dev/null
+++ b/ci/scripts/utils/get_config_var.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+
+import os
+import argparse
+from wxflow import Configuration
+
+
+def get_config_vars(var_names, config_path):
+    """
+    GET_CONFIG_VARS Get configuration variables from a config file or directory.
+    Parameters:
+    var_names (list of str): The names of the configuration variables to retrieve.
+    config_path (str): The path to the configuration file or directory.
+    Returns:
+    list of str: The values of the specified configuration variables.
+    """
+    if os.path.isfile(config_path):
+        config_dir = os.path.dirname(config_path)
+        config_file = os.path.basename(config_path)
+    elif os.path.isdir(config_path):
+        config_dir = config_path
+        config_file = 'config.base'
+    config = Configuration(config_dir)
+    config_data = config.parse_config(config_file)
+    return [config_data[var_name] for var_name in var_names]
+
+
+if __name__ == "__main__":
+    """
+    Main entry point for the script.
+    Parses command-line arguments and retrieves the specified configuration variables.
+    """
+    parser = argparse.ArgumentParser(description="Get configuration variables from a config file or directory.")
+    parser.add_argument("var_names", nargs='+', help="The names of the configuration variables to retrieve.")
+    parser.add_argument("config_path", help="The path to the configuration file or directory.")
+    
+    args = parser.parse_args()
+
+    var_names = args.var_names
+    config_path = args.config_path
+
+    values = get_config_vars(var_names, config_path)
+    print(" ".join(values))