The mdl files are for the ships, anomalies, stars, etc. They're animated models. The file format includes the bitmaps and information about the number of frames, animation name, etc.
There's a link up in a sticky thread for a ship encoder now. We may be expanding it to encode the other objects as well. It's a modified version of the program that we use to encode our graphics, to skip a bunch of the steps that we have to go through.
The interface files are saved as mtd files. They're rather more complicated to make and we don't have a program like SkinStudio for our interface. It's an extreme PITA to create a screen, even if you know photoshop well.