First, put in the area you want to engrave a piece of anodized aluminum. Like this you do not engrave the work area too. Alternatively, you can also work with the honeycomb table. Then, you set the mirror with the mirror side facing up into the laser.
After that you can engrave the mirror reflective side up side through the glass with your desired pattern. Glass does not react with the fiber laser, and so only the mirror layer is removed by the laser. The glass itself is not scratched because it reacts only to the wavelength of the CO₂ laser source.