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The native file format for Milkshape 3D-models is the ms3d-format. This file format is structured in the following way:

   * Header
         o "MS3D000000" followed by version number (ver. 3 or 4)
   * Vertex Data
         o Coordinates for the vertices
   * Triangle Data
         o Pointers to vertices, as well as surface normals
   * Group Data (object/mesh)
         o Group name and pointers to triangles
   * Material Data
         o Color details
   * Bone data
         o Animation data

More details here: