This very detailed tutorial was prepared by Nabgha Farhat, Brigham and Women's Hospital. It describes, step-by-step how to extract specific data form CT scan and convert them into format from which it can be 3d printed. She isolated portions of the mandibular bone and the temporal bone for the model. Freee and open-source Slicer software was used.
Data was acquired with: http://en.wikipedia.org/wiki/Cone_beam_computed_tomography
Tutorial has several chapters:
Introduction to the 3D Slicer interface
Loading data
Volume rendering and cropping
Creating label maps
Creating surface models
Saving data in file formats appropriate for 3D printing
Link to Slicer:
http://slicer.org/
http://wiki.slicer.org/
Slicer is a free, open source software package for visualization and image analysis. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X.
Luis Ibanez made a post on KitWare blog, describing the process of actually printing this object:
http://www.kitware.com/blog/home/post/591
For other medical field 3d printing applications see:
http://diy3dprinting.blogspot.com/search/label/medical%20applications%20of%203d%20printing
Source:
https://www.youtube.com/watch?v=MKLWzD0PiIc
BTW: yes, you can 3d print your own skull if you have a CT scan of it ...