Solidworks: Coincident or interfering geometry when saving assembly to STL
Solidworks has means for detection and eradication of these errors. If there's unwanted intersection, then you can either separate the parts or merge them (by saving assembly as a part). If you work with SLDPRTs, then use mating options correctly, avoid manual mating, make sure that the design of your components actually allows them to mate without intersections and you'll have no problems. If you work with parts that are loaded from STLs though, then you'll probably have a lot of these errors when trying to align parts. Solidworks can't work smoothly with STL models, alas, you'll need some other tool, MeshLab or something.