Another method, though more more complicated than what Mark suggested, so definitely try that first, is to use a probe to measure the height of the material. Set it to measure the heigh over a grid of points and record the values. You then take that matrix and use it to offset the Z co-ordinates in your engraving G-code to compensate for variations in height. Clearly it's effectiveness depends on the flatness to number of points ratio. It is apparent if you search on google that this method is effective when engraving PCBs which is a similar process, I believe your material is a similar thickness?