I wanted a 3d case to protect my miniSpartan6+ fpga development board, but all of the cases I found online didn't have openings for the GPIO headers. I decided to start from scratch and make a case for the board with OnShape, an online 3D CAD tool. I had the enclosure manufactured by Shapeways, and to my dismay, when it arrived, the board did not quite fit. I removed some of the "alignment" pegs from the box, and since the fit between the board and the box was so snug, I didn't actually end up needing them anyway. The enclosure finally fit after some encouragement involving a utility knife.
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