Clear? No. When clear plastic gets foamed, the product looks white. There is packing foam like that.
Is it a 60% in a standard Poker-compatible tray-style case? Then the PCB will be screwed to standoffs: instead of using foam, you could put rubber O-rings on the standoffs.
Or is it a PCB suspended from a plate? Then foam won't do much, as most vibrations will be transmitted through the plate and not the PCB.
Another silencing mod people do is to put foam between plate and PCB (3.5 mm), but it is more work cutting holes for all switches and I dunno how much effect it will have compared to the other methods.
In any case, underglow/sideglow is around the perimeter. You could perhaps use a smaller rectangle of white foam inside that perimeter, and the white sides of the foam will reflect the light.