diff --git a/PyFluxPro.py b/PyFluxPro.py
index 8e56d42..e67f860 100644
--- a/PyFluxPro.py
+++ b/PyFluxPro.py
@@ -34,9 +34,10 @@
 
 # now check the logfiles and plots directories are present
 base_path = pfp_utils.get_base_path()
-logfiles_path = os.path.join(base_path, "logfiles", "")
-plots_path = os.path.join(base_path, "plots", "")
-dir_list = [logfiles_path, plots_path]
+# Create logfiles folder on current directory, so that this can be outside
+# the PyFluxPro folder.
+logfiles_path = os.path.join(os.path.abspath("."), "logfiles")
+dir_list = [logfiles_path]
 for item in dir_list:
     if not os.path.exists(item):
         os.makedirs(item)
diff --git a/scripts/pfp_utils.py b/scripts/pfp_utils.py
index 18a6095..c9bb321 100644
--- a/scripts/pfp_utils.py
+++ b/scripts/pfp_utils.py
@@ -2051,8 +2051,9 @@ def get_base_path():
         base_path = sys._MEIPASS
     else:
         # running as a script
-        base_path = os.path.abspath(".")
-    return base_path
+        #base_path = os.path.abspath(".")
+        base_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+    return base_path    
 
 def get_cfsection(cf, label, mode='quiet'):
     '''