Oops! We've all done it, though many PCB vendors will automatically mask out any silk screen that overlaps exposed copper pads. It might be worth adding a note to your drill drawing to require vendors to do this for you in future.
Are you going to solder the board straight away? If so then it doesn't matter too much if you remove some of the surface plating in the process of removing the silkscreen, as its main purpose is to prevent oxidation.
I'd start with a fibreglass pencil, or possibly just scratch it away with a sharp scalpel. Shouldn't be too hard IMHO.