"Thanks" works just fine for me. Then brush it off - segway into whatever your usual ramble/banter/conversation material is. I do the same whether it's a girl I don't know or one I'm dating when I get compliments on my body or my third gorilla leg. I'm slightly above average looking, but I still get this from girls in the 6-8 range. It's like anything you hear, don't react or take the compliment too seriously whether it happens often or not.
Vice-Captain - #TeamWaitAndSee