So you will be cnc machining both the recesses and the inlays?
Then you mention "Fit Perfectly".

There are other factors involved in doing this kind of material combining. It isn't something that you can just jump right into and get a perfect result on the first try. Hopefully you have already walked the walk.
CNC will make this kind of work a little easier by getting the parts close to what you need. Possibly perfect for you.

You will always have a crack between the materials. I would not shoot for a perfect fit, but rather a relaxed fit and fill the gaps with epoxy. This will allow at least some different expansion between the materials without buckling or busting out a seam.

If it is not too intricate, you may pull it off with your current gantry. The bottom of the recesses will be covered, so not critical for surface finish.