If you are going to design the enclosure yourself you'll need a 3D package such as Solidworks or Inventor to do the job properly.
Then the fun starts.
First off I'd look at this site, lots of good basic design guidlines.
For prototype models look at someone like ARRK, there are numerous methods of producing rapid prototypes, and depending on the required use of the prototype will determine the construction method (SLA, SLS, FDM etc).
Of course you'll need a 3D model to get your prototype done.