What format is the non-native part?
After importing it into SW, use the Import Diagnostics tool to help fix the model.
That is going to be really tough to do. Feature Works is good on the easy stuff like plates and holes and simple fillets. It doesn't do well on organic shapes made with Lofts, Boundary Faces, or Fill Faces.
If you can't get the shape you want with Move Face, then you are probably going to have to build it from scratch, using the imported model as a guide. This is probably going to require you to learn a whole lot about surfacing. Matt Lombard's Surfacing Bible and Ed Eaton's Curvy Stuff tutorials http://www.dimontegroup.com/Tutorials/SolidWorks_Tutorials.htm
will be a big help.
ps. Build your new SW surfaces over the top of the imported model, matching it as closely as you can, but keeping in mind how you want to change it. This may require you to build some of it in ways that don't match the imported model very well. This shouldn't be a big deal, since your new part isn't going to match completely anyway.
Message was edited by: Jerry Steiger