When I was making guitars I had a set of plug cutters. These cut a clean round plug out. They could also be used to cut plugs from a donor shell and with careful installation they would be just about invisible...Taper plugs are ok but they only fit tight on one side. If you like those, get a taper reamer to prep the hole first.
Hi J!m !
Unfortunately, i don't have plug cutters, so i had to (very carefully) saw off the exposed wood from the dowels peering through the lug screw holes..It was tricky, but i did it as close to the shell as i could, and sanded down the remaining dowel tip with some 220 grit sandpaper, and that did it. Next resto project that requires hole plugging, i'll be sure to pick up a set. ;)
cheers,
Rob