I don't think you need to do anything. Print it and see.
Despite what the screen shows, when I print, the holes are completely clear. The problem I have with Eagle is that the green pads come out slightly shaded/hatched rather than solid black. (If your print doesn't have clear holes... hmmm, did you maybe draw in wires rather than route signals?)
I keep meaning to try changing pads to a different color, but so far I have succeeded in forgetting this every time, and I just deal with ratty pads.