I made a layered topo map a year or so back. Here’s a couple of tricks I figured out.
Print some Guidelines
One trick I figured out was to put all the layers in one file, and color code them. Then, when printing, I would select the lower color N for cutting and the color N+1, above, to be etched into the lower piece. When it came time to assemble the layers, I used the etched lines to get the layer above properly aligned - much easier than eyeballing it.
Save Wood When Cutting
Note you are limited to 7 main colors (plus white for the background) that the laser will recognize. I cycled through those colors and reused them in order. Then, I cut layer N and N+7 from the same piece of plywood. This saved a lot of wood, as the higher contours are relatively sparse. Thus, I was able to cut 12 layers out of 8 pieces of wood (7 colors + the base layer).
Use a Spreadsheet to Save Mistakes
I put together a spreadsheet which told me which color to etch and which to cut for each layer. It’s easy to lose track without memory backup.
Save the Frame for Last
I waited until all the pieces were assembled and finished before I cut a frame to fit. That way, any slight shifting of the layers won’t keep the piece from fitting into the frame.