Do you mean the ones that bolt through the wheel arches? You can either just fit a nut and bolt with a large washer, or get a standard rubber grommet of the right size. But the carpet will have been squashed flat on the inside, and quite probably stained with rust from the bracket, so it will never be quite pristine. There are also other holes punctured in the headlining in order to access the upper mounting points, and rear grab handle if fitted. I'm not sure what you can do about them - try and glue them up or fit a dummy bolt with washer perhaps.