Just to clear up a little confusion, I engraved the gemstones but I didn't actually build them. These were lab-grown gemstones, technically real rubies and sapphires but not natural rubies and sapphires. Gem Select has a nice, balanced explanation of synthetic gem stones here if you're curious. It's informative and respectful, but they don't trade in synthetic gems so they aren't pushing a product.
The clear plastic 'windows' in the Rox Box were literally 3D printed already-assembled by building the majority of the puzzle using white material, then switching to transparent material for the last few millimeters. This is how the model looked when it came out of the printer, embedded in a solid block of white material with a few layers of clear material (at right).
After I cleared the material from the inside of the models I could see through the windows, but the parts were still embedded in unused support material from the build process.
Peeling away the material around the exteriors revealed the finsihed Rox Box parts, complete with their transparent windows for the top and bottom. This is how the puzzle box looked the first time I got to see it!