diff --git a/src/imcflibs/imagej/projections.py b/src/imcflibs/imagej/projections.py
index c25107cf122a0933d84aeea4b993e6bb7ef863ec..a598b82dbe30fc1beac653bfa9024a2efb3b1f1a 100644
--- a/src/imcflibs/imagej/projections.py
+++ b/src/imcflibs/imagej/projections.py
@@ -52,7 +52,7 @@ def create_and_save(imp, projections, path, filename, export_format):
         A list of projection types to be done, valid options are 'Average',
         'Maximum' and 'Sum'.
     path : str
-        The path to store the results in.
+        The path to store the results in. Existing files will be overwritten.
     filename : str
         The original file name to derive the results name from.
     export_format : str
@@ -69,5 +69,6 @@ def create_and_save(imp, projections, path, filename, export_format):
         export_using_orig_name(proj,
                                path, filename,
                                "-%s" % command[projection],
-                               export_format)
+                               export_format,
+                               overwrite=True)
         proj.close()
diff --git a/src/imcflibs/imagej/shading.py b/src/imcflibs/imagej/shading.py
index e976b6965756a646d09bb1d9090ff0ee7c8aec50..5f056af84cd04d8885e511a31ba52a525db9d08a 100644
--- a/src/imcflibs/imagej/shading.py
+++ b/src/imcflibs/imagej/shading.py
@@ -60,7 +60,7 @@ def correct_and_project(filename, path, model, proj, fmt):
         The full path to a multi-channel image stack.
     path : str
         The full path to a directory for storing the results. Will be created in
-        case it doesn't exist yet.
+        case it doesn't exist yet. Existing files will be overwritten.
     model : ij.ImagePlus
         A 32-bit floating point image to be used as the shading model.
     proj : str
@@ -75,7 +75,7 @@ def correct_and_project(filename, path, model, proj, fmt):
 
     orig = bioformats.import_image(filename, split_c=True)
     corrected = apply_model(orig, model)
-    bioformats.export_using_orig_name(corrected, path, filename, "", fmt)
+    bioformats.export_using_orig_name(corrected, path, filename, "", fmt, True)
 
     if proj == 'None':
         projs = []
@@ -100,7 +100,8 @@ def process_folder(path, suffix, outpath, model_file, fmt):
     suffix : str
         The file name suffix of the files to be processed.
     outpath : str
-        The output folder where results will be stored.
+        The output folder where results will be stored. Existing files will be
+        overwritten.
     model_file : str
         The full path to a normalized 32-bit shading model image.
     fmt : str