I've discovered that some STL files can be reverted to STEP files (solids) which can then be imported into a solid modeling application, Creo in my case, and modified in some ways.
I used FreeCAD which i run on Ubuntu 16.04. I import an STL file into a FreeCAD session, run the mesh analyzer, auto-repair any problems found, convert to a shape, then to a solid and output a STEP file.
Then open the STEP file in Creo, and it's not paramtetric, but you can drill holes and add and subtract material from the solid.
I also tried reverting some STL files used for fuselage sections in a 3dlabprint.com r/c plane but, alas, these files, despite printing well after slicing in Simplify3d had too many problems to convert.
Have questions or comments about Simplify3D, Slic3r, Cura, Reptier, etc? Or wondering about which CAD software to use...discuss it here...
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Depending on size there are definitely different programs that can do this(Solidworks and Fusion360). Fyi those are just the ones I have experience with in the last few years creo may be able to do this as well(about 10 years since I last used). There are multiple tutorials online that can walk you through using the conversion of stl files directly in the cad software. This has usually provided me with the best results.