Model Generation : Cleaning up 3D models with Geomagic
Import the model into Geomagic.
You can select any polygon by using the selection tools (Edit -> Selection tools) and the left mouse button. There are two modes (found under Edit or in the Toolbar (see screenshot)).
select visible (ctrl + V): selects only polygons that are visible ("surface" polygons)
select through (ctrl + G): selects all polygons encompassed by the selection tool

Save repeatedly!

Geomagic lets you undo only the last step and it has a habit of crashing if you do something illegal.

Remove pieces not belonging to the bone

If you have bits and pieces not belonging to the bones floating around in space, use Polygons -> Make manifold -> open.

Fill holes

Holes in the bone can be filled by using Polygons -> Fill Holes. Note that only 'open' holes can be filled that way (see screenshot).
If the hole looks similar to the image below, select the adjoining polygons with the selection tool. Go to Polygons -> Fill Holes -> Fill Method 'Fill' -> Deselect 'Apply Boundary Cleanup' -> Click 'Fill all' -> Click 'OK' if you like the result, click 'Cancel' if you do not. Once you hit OK, you cannot undo!
If the hole resembles a tunnel, e.g. forms a surface, you have to first open it up. Select the hole area (use select visible!), press delete (hole opens up) and go to Polygons -> Fill Holes -> Fill Method 'Fill' -> Deselect 'Apply Boundary Cleanup' -> Click 'Fill all' -> Click 'OK'. Again, once you hit OK, you cannot undo.
Sometimes, Geomagic refuses to fill a hole and crashes every time you try it. If that happens, try to do the following (save your work first!): Select the hole, go to Polygons -> Fill Holes -> Fill Method 'Create Bridges". Create Bridges across the hole (do not worry if it looks funky). Once you creates a couple of bridges, click 'OK'. Then select the polygons of the hole and a bit of the surrounding area and delete it. Try filling the hole again using the 'Fill' method.

Smoothing bones

Select the bone's area you want to smooth and use Polygons -> Repair -> Remove spikes. (Smoothing over the complete bone usually flattens out condyles or other anatomical structures.)

Remove inner core

Bones with a large medullary cavity tend to have two surfaces; an outer one and an inner one. The inner one is not visible in Geomagic, but it can create problems in Maya, especially when you want to do Rotoscoping. To remove the inner surface, make sure you have 'select visible' enabled. Select all polygons of the outer surface by repeatedly rotating the model and selecting the whole structure. At the end, all outer polygons should appear red. Go to Edit -> Reverse selection. Now the surface should appear white, whereas all polygons of the inner surface are selected. Press delete to remove inner core.

Save model

Geomagic's saves as Wrap File (.wrp) by default. For Maya, you need to save your models as Wavefront Files (.obj).

Shortcuts and Keys

alt + RMB translate
ctrl + RMB rotate
MMB rotate
MMB + scroll zoom
alt + LMB change light source
ctrl + C deselect all
ctrl + D center