To make it a little more interesting, we didn't want to add any elements to the photo later in Photoshop. We could tweak the images a bit and remove stuff, but nothing could be added. This meant that the logo had to be really in there.
Thanks to Adobe for letting us test an advance copy of Photoshop CS5 to get this effect quickly and easily.
Step 1: Make the logo
The letters were lightly cut so that the protective layer on top was cut through without digging very deeply into the acrylic. This makes it so that you can remove just the letters and the rest of the space is still covered.