I made this project over at TechShop (http://techshop.ws/).
Step 1: Materials & Tools
CorelDRAW or Adobe Illustrator (trials available)
1 3/8" 18 x 12" sheet of plywood
Step 2: Designing the Box
Open the pattern in Illustrator and select one of the pieces to make the front of the box. On that pice add a 4.5 x 3 inch rectangle where the matrix will stick out (it's going to be a snug fit). I also added two smaller rectangles, as you can see in the picture; I decided to add those to affix to the top and bottom of the interior to hold and support the matrix firmly in place.
Step 3: Cut Out the Box!
(Ignore the extra cuts in the picture, I was being frugal and working on multiple projects.)
Step 4: Put It Together and You're Done!
After that, just figure out which piece goes where and start gluing, making sure that you don't glue the front piece where the matrix will be so that we can easily remove it and any other electronics inside. And that's it! If you need a refresher on wiring your matrix then consult the Adafruit guide.