My CAD is pretty rudimentary; but I've had a go at an alternative to 3D printing, which should be more amenable to assembly with basic hand tools (if you don't mind getting your hands dirty and can cut a reasonably straight line) or relatively simple machine shop operations:
The basic idea is a simple 'sandwich' design. On the bottom is a baseplate, 120mm by 96.5mm (so, if centered, the UDOO PCB has 5mm of material on each side for a modicum of protection, without making the ports hard to reach. The baseplate has holes matching the locations of those on the UDOO PCB. If you want to use standard PC motherboard standoffs, these should be 6-32 tapped, if you find it easier to source the standoffs used in D-sub connectors (eg. VGA, serial, DVI) you'll want 4-40. (The attached baseplate file has 2.2mm holes, which should suit 4-40 screws, 6-32s would be better off with more like 2.7, with the caveat, in both cases, that all metal screws are somewhat self-tapping if you use acrylic or polycarbonate and all steel screws are slightly self tapping if you use aluminum and a little violence...)
Above the baseplate and the standoffs goes the UDOO itself.
The top plate is similar to the baseplate; but cut to try to expose the headers without totally sacrificing protection. The uploaded rough-cut has no tolerances for the 2.54mm headers(so those cut-outs will have to be a bit larger, depending on the tolerances of the process); but the cutout area on the bottom right, while slightly arbitrary, should expose all the headers located there.
The whole assembly is then secured by screws driven down through the top plate and into the headers on the bottom plate, with nylon spacers of suitable length(still to be measured) keeping the top plate an appropriate distance from the UDOO(whether you want the 2.54mm headers slightly above the top plate, perfectly flush, or slightly sunken can be ajusted to taste by trimming the spacers).