Gian Pablo of Makerbot was a little daunted at first when he was tasked with printing an enormous complex 2/5 scale crocodile skull. He used a CT scanned crocodile skull from the University of Texas Digimorph project. Laser scanned and MRI derived files can be full of junk geometry and self-intersections, but with a few deft repairs you can get most files print ready in less than an hour.
He took his model into the free STL suite Netfabb for some cleanup, scaling, and slicing (this would be the point at which you could take your model into your own Personal Factory to print). Netfabb has a convenient auto-repair script that can handle most basic geometry problems and generate manifold surfaces. He then used Makerbot’s own free program ReplicatorG to generate code for the Makerbot.
After that all that was left was to print the skull in stages, and glue the resulting parts together.
You can read the full details over on Makerbot’s own blog.