There is no way to manipulate a .stl file because Pro does not see it as a solid instead a bunch of small faceted surfaces. Is there any way you can get an .igs or .stp file? You can import these into a part and hack them up any way you like.
Generally STL files cannot be edited in normal CAD softwares But there are some special softwares that can give u the functionality to edit the stl and add some features.
Almost all reverse engineering softwares have the capablity to handle stl data.