SolidWorks has some pretty smart import functionality, so I think that would work pretty well. How many files do you have to convert?
You could try to create a macro or addin for this. There are many people here that can help you get started, we just need some more info on your requirements.
For a customer I've been working on an addin that (amongst many other things) imports STEP files, runs Import Diagnostics and exports a modified STEP file. I can probably adapt that code to import and clean up STL files.
Are you aware the topology of stl files is triangular planar facets?
Can you attach example stl file here?