Hey Ricardo,
For any mesh on the simulation side (i.e. Collision and Fem meshes) only the ply file format is supported. The Fem mesh information is not read from the geometric ply information (i.e. the face element) but from a special fem element in the ply file that indicates the type of Fem that is being read (1d_element, 2d_element, 3d_element). As I am looking at the sample files in Physics/Unittests/Data/PlyReaderTests I see that we did not document the format very well if you would like I can write up a better description. The reason we chose ply is exactly for the extensibility in this case and the ability to take on extra elements without having to break the file format.
For graphical objects any format that is supported by your OSG build can be used. The long term plan (this means we are not currently working on it) would be to utilize OSG as a model converter that lets us generate an OSS mesh from any scenegraph the ground work is there through the Graphics::Model class that could encapsulate the access to an Graphics::OsgModel without having to expose OSG to the rest of the system.
Currently there is no fixed toolchain for authoring FEM, Julien the physics lead should be able tell you more when he is back from vacation next week. I think he uses TetGen (
http://wias-berlin.de/software/tetgen/) and then integrates the information from that tool into the ply file. With the graphics and structural information separate, you can use the same ply file for the FEM and the graphics and just transfer the FEMs positional information to the graphics mesh as is done in the Stapling example.
We are currently in the process of extending and refactoring the way FEMs are being read and built, the added flexiblity will be in specifying which kind of fem element should be constructed, the type will be less generic than , we would love to hear about any requirements on your side, or see contributions. (Sorry for the plug there)