Glass can be cut into any shape you like. It is not easy to do, but with lots of practice and a little patience, it can be done. Cutting a square hole in glass requires a little more preparation than some other cuts. Cutting square holes in glass requires that the glass be scored or cut first, and then the glass is broken along the score lines. It takes a very delicate touch to be done correctly.
Build a small mound of putty on the glass where each corner of your square is to be located, and make a hole in each. Fill each hole with mineral turpentine. Drill a hole through each mound and then through the glass with your glass bit. It is easiest to use a drill press because you will not have to steady your hand and you can concentrate on keeping the glass still.
Place the glass on a level surface. It is always preferable to place it on a hard surface with a piece of carpeting on it. Dip your paintbrush in turpentine and then paint the outline of the square with it. This will lubricate the glass and make it easier to score. Run your glass cutter over the outline of your square to score the glass. Use your wooden straight edge to make your line straight. Connect each of your four holes with these scores.
Tap the glass with your finger gently until your square falls out. Exercise extreme caution in removing the rest of the glass if it breaks out in several pieces.
Ensure that you wear safety glasses while you are cutting glass. This is particularly important when you are using turpentine as a lubricant.