I A Few Small Spots On My Penis That Have

I a few small spots on my penis that have a little opening or black dot in the middle. It stung to remove the small black dots and after there seemed to be a smal hole left behind in the middle of the spots. What could these be and how can I treat them? Shouldn't be an STD because my girlfriend and I have both been tested and only been with eachother for past several months.