I assume you used the stuff that already had the foam bonded to it. I cut it with a good scissors.
Are you talking about trimming it after it's up on the roof? If so, you need to leave it a little long and then push it down into the rubber seal. I use a heavy putty knife with the corners ground off to do that. That will leave you with a nice clean edge.
No one lives forever, the trick is creating something that will.