Pro/Engineer, CATIA and Rhino can all import STL data and generate surfaces from it...Look at software by Geomagic as well.. We use Pro/E's Reverse Engineering Extension, which uses Geomagic's software.. We use it to generate surfaces from STL files, point clouds, and scan data.
These are all a far cry from being free but they will get the job done. Last time I looked at Rhino there was a free demo of the software, which lasted for 20 uses or something.
-Mark Morreale
Application Engineer
Torgon Industries Inc.