I just started fusing glass. I have a microwave kiln. Everytime i make a piece the back side is rough. I saw other people at a fair that made the same thing and the back side of their pieces were smoother.
Are you using the kiln paper supplied with the microwave kiln? Is it by Fuseworks? This thicker paper will impart a texture to your glass. You can try other kiln paper to see if that gives you the look you want.
If you kiln shelf is smooth, you can use thinfire ( a Bullseye product), if you have the coarser paper, you can smooth it by adding kiln wash to it and smoothing it level. If you are working small, you can grind and polish the back to get it smooth, too.