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I agree with everyone above, but will offer another possibility. When I had tried STL files, I had terrible results. Maybe there were some small visible portions, but most of the mesh didn't show up.

What I ended up doing was installing Blender, which I highly recommend. In Blender, all I did was import STL, export Collada, and then use the .dae mesh in my URDF. This solved all of my problems.

I did have to re-center the origin of my mesh in Blender so the joint would show up in the right place (thanks AutoCAD for changing the origin :P ) but luckily did not have to do any scaling.