I don't have 10.3.0 to test, but checked it with 10.3.1 and it worked as expected. Are you using the clip_analysis tool? Clip—Help | ArcGIS for Desktop
Python snippet
# Replace a layer/table view name with a path to a dataset (which can be a layer file) or create the layer/table view within the script
# The following inputs are layers or table views: "GMU", "ClipPoly"
arcpy.Clip_analysis(in_features="GMU", clip_features="ClipPoly", out_feature_class="C:/_temp/clippedGMU.shp", cluster_tolerance="")
Some things to check:
- Are you maybe trying to put the .shp file into a .gdb instead of just a folder?
If trying to make a featureclass in the .gdb, it will not be a shape file and should not have the extension. As Dan mentioned, that might be a better choice. - Make sure to keep the output name short, no spaces or special characters. Underlines should be ok.
- the "Clip Features" needs to be a polygon
- It help is the "Clip Features" is in the same projection as the features you plan to clip. If a proper projection is assigned to both, it may work, but since shape files need a .prj file, and sometime they are not the newer standard names, that can cause issues (although that would not be why you get .shp.shp)
Check those things out and see if that fixes it. If you are still getting a double .shp, give a snapshot of the command window and hoe you have it filled out. Although I tested in 10.3.1, I had 10.3.0 for quite a while and don't remember any issues, just fyi.