This video demonstrates how the best way to approach STL File Repairs is to catch them at the CAD stage when possible, when the geometry is still intelligent and you have access to tools to make the models watertight, before the geometry is degraded into non-intelligent triangles.
For more further information on how you can nip geometry problems in the bud by solving them at the CAD level, read the full story at http://TransMagic.com/Avoid-STL-File-....