I built one of these:
http://www.instructables.com/id/Pong-Word-Clock/
and then I needed a case to put it in. I had just got my 3D printer, so this is my first project designed from scratch. The design includes cutouts and standoffs for the LED panels and also standoffs for the Freetronics Eleven Arduino compatible board that I used for the project. I believe that any Arduino Uno compatible board will also fit the standoff pattern.
You can edit the design using a DXF file editor and OpenSCAD. The basic layout has all been done using 2D DXF files. Each layer that needs to be a different height uses a separate layer in the DXF file. Each layer is then "extruded" to the correct height in OpenSCAD. All extruded objects are added together to make the 3D object.

I printed my box in ABS using 0.4mm layer height and solid infill. Turn on Support Material so that the rectangular cut-outs are nice and neat.
To join the three sections together I used a single piece of clear 3mm perspex across the back.