Segmenting elements from a CT scan
The XROMM wiki maintained by Brown University has an excellent series of tutorials on creating surface models from CT scans (segmentation) so I will just link to them here.
The following tutorials cover segmenting and creating surface models in either Horos (free, Mac only), 3D Slicer (free), or Amira.
And the following tutorials cover cleaning surface models in either Meshlab (free) or Geomagic.