There are marking pens that can differentiate currency paper. Most often used on $50 and up, but can be used on any bill.
http://www.centercoin.com/coin_supplies/counterfeit_detector.htm <-- Check it out
Thanks. I buy coffee every morning at a Mcdonalds. If I pay with a twenty they always mark the bill. I always wondered why but never asked. Now I know. I'm glad the ink has always been amber colored.