SealMan,
It's going to be your job NOT to damage the rubber roof material... I have used both a plastic scraper and a Metal putty knife to remove the caulking around vents and seams.
Begin on the hard surface of the vent flashing.. prying the material off the surface... when you've enough to grasp... gently start lifting as you work the blade under the caulking material. Your going to quickly see how it comes off.
Clean the area well but be careful not to use any cleaner that will damage the rubber roof material. Petroleum based products will damage the rubber roof.
Good Luck on the project !