This is a OpenSCAD model of a project enclosure box similar to the black ABS ones at Radio Shack. I modeled this specifically to house 60mm x 80mm prototype boards, but the parameters can be set to work with any size or height clearance.
I have not yet had a successful print with this size on my Makerbot, mostly due to ABS curling -- something I hope my forthcoming HBP kit will solve. I have printed smaller sizes and aside from the PCB mount holes being sometimes occluded, it seems to work well in various dimensions. I expect I may need to add a few extra tolerance parameters for "wiggle room" as this design assumes perfect printing.
Load enclosure.scad in OpenSCAD
change parameters to fit your boards dimensions, mounting holes, and height requirements
Design -> Compile and Render
Design -> Export to STL
At the bottom of the file, comment out project_enclosure() and uncomment enclosure_lid() -- if you need a lid. Then repeat the last two steps.
Drill/Carve out screw holes