Well looks like I'm a little late to this...
But back when I did German armour years ago I used an Atlas snap saw, you can find it on the model railroad section of the hobby shop. Any razor saw should work though.
I coated the side of the model with Squadron green or white putty and then would drag the saw flat side first though it making the waffle pattern. Jog the saw every centimeter or so. And wipe it off when it gets clogged too badly. Keeping the saw wet with rubbing alcohol will keep the putty from sticking to it.
I'd assume any other putty should work, for example Perfect Plastic Putty with water to keep the saw from sticking. Tamiya makes a set of tools for doing zimmerit. I have a set but I haven't used them. Last kit I used zimmerit on was a Dragon Tiger II, which I used the pre-cut ready made zimmerit.