Here's a low-poly version of the final model. Click to view in 3D (Click/drag rotates, shift+drag pans)

Step 1: Import mesh data into Rapidform (Insert -> Import...)

Step 2: Draw reference planes to help align the scan in space. (Use the Extract method to draw a plane along the bottom chunk of scan data. Then use the Mirror method to draw a symmetry plane down the center of the skull. Draw a seed plane first using Draw Line to give the Mirror function a rough idea of where the center is.)

Step 3: Use Interactive Alignment to orient the scan in space. (Select the first two planes as the Plane and Vector options.)

Step 4: Use Healing Wizard to delete junk data

Step 5: Use the Fill Holes tool to fill holes. Use Fill Gulf and Bridge option to fill in large holes in stages.

Step 6: Use Boundary Extrude to fill in the nasal cavity. (This hole is too big and detailed to use Fill Holes.)

Step 7: Use Global Remesh to make all the mesh faces the same size. This will make it easier to edit the extruded portion.

Step 8: Use Smart Brush to add detail to the extruded portion of the mesh. The Deform option pushes by default, but will pull if you hold Ctrl.