CO2 lasers can (40w included) can mark glass, but it is not actually etching the glass. When a CO2 laser's focal lasing energy is at the surface, or just past the surface of glass, the air inside that portion of the glass will expand and cause a tiny crack. This gives the appearance of etched glass, but not with the same fineness of etching from, say, sand blasting or acid etching (with hexafluorosilicic acid). If the laser "etching" of the glass is not to the fineness that you desire, you can laser cut the adhesive material used in the acid etching process as an alternative.
You also need to consider the glass you are using. I have learned that not all glass is created equal. Some glass will work well for this (dollar store glass we have tested and works well), and some will not. I believe that lasing tempered glass will probably give some interesting results.
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Will the 40W CO2 laser etch glass?