I just got a big sheet of eggcrate from Home Depot and ask the guy what would be the best way to cut it? He told me a circular saw with a fine blade; but I am a college student in an apartment, hours from home, and the sharpest cutting tool I have is a pair of Scissors.
It doesn't have to be perfect. The scissors should work. Just leave yourself plenty of space on the sides so the rougher edges don't scratch anything. Most of your weight will probably be placed in the center of this anyway.
For simple shelves for corals I have used a pair of needle nose pliers to just break the connection down a row. I was surprised at how neat it actually was. Just grab a piece and twist. It snaps right off.