We’ve been using solidworks in combination with a plugin called XTract3D, to build clean models from 3D scan data. Works great, and is what we were missing to get it done in Solidworks alone.
Here’s their site:
Learned how to do it, and how far you can go with it from a free training video they have on their site. It’s an in depth video, but it teaches a lot, worth it IMHO.