Almost all motherboards are made to a standard ATX variant, the dimensions are freely available. If you have the skill and time as stated above, you can build anything to be the chassis, so long as you design it with the standard dimensions in mind.
If you're using a non-standard board, getting the proper clearances and stand-off placement might require getting the board before building, just to take measurements. (Mostly for server/rackmount boards. I'm looking at you, SuperMicro. O_O)