How to Reformat Surface Meshes?

I have a bunch of surface meshes (.stl format) extracted from CT scans. How do I convert them to a supported file format?

Should I attempt to extract something besides meshes from my tomographs (like a numbered array of surface elements)?

To create a set of data suitable for display in ProfilmOnline, the data must be represented as a set of height values spaced on a regular grid. See this post for additional info.