Use acetone on a q-tip or paper towel. Then remove any acetone smear with windex, alcohol, or the similar glass cleaning solution. I do this a lot when I mark and cut out designs in Ultracote(or heaven forbid, monokote). It works well.

Alcohol was mentioned above. Sometimes it works and sometimes it doesn't, depending on the marker. Try it first, if it doesn't work well, then use the acetone.