Step 1: Design the template
This one is designed such that you can cut it from one piece of material and then snap in the interior pieces to do different layers. Since you never have to remove the first layer, the subsequent layers are already aligned.
If you are going to laser cut the template, make sure your design is in a vector format. Programs such as Adobe Streamline can turn bitmaps into vectors.
Step 2: Make the stencil
I elected to laser cut a stencil from 1/8 thick acylic. I wanted to reuse the stencil and have relatively small, sharp features.