To evaluate the acoustic effects of the morphology of bats, my colleagues and I build 3D models based on Micro-CT data. Details about this procedure can be found in De Mey et. al. 2008.
The first step in building a new model is to perform a high resolution CT scan of a bat specimen. The slice data is reconstructed to 3D data. Finally, using medical imaging software, a 3D model is created from the 3D data. We can also study the internal structure of the bat's nose/mouth cavities (see for example our SAB2010 contribution).
The following movies are from the supporting material from our Frontiers paper.