It should be as easy as creating a solid square in a cad software (freecad for example), then in ESTLCAM just using 1mm (maybe 2mm) depending on how flat it already is engrave, and set the router bit perfectly on top of the wood (flush) and let it go. it will go down to the designated depth and engrave out the whole thing.
I plan on doing that simply to make my bed perfectly level, but you have a great idea about putting in a piece of glass. thats very smart. If i turn mine in to a 3d printer i will do that too (except ill make mine huge. i already have a 12×12 3d printer haha