Quoted from Rdoyle1978:

It's doable; I did it on a fully Kruzman cleared monster bash PF. Use a dremel with a very precise tip to get the clear out of the holes entirely, including the countersink area (espcially there). this gives the nail the clearance to actually sit flush. if there's any clear left, it will sit proud of the playfield.
Get the nail started by pounding it in with assistance from a piece of wood (don't use a hammer directly ), and towels around the playfield to keep from any misses. Get it in about halfway
Then find a lock nut to screw onto the nail from under the playfield to pull it through the playfield instead of trying to pound it in directly from the top

Quoted from Timerider:

Unless it's an odd angle; those don't look "flush" in those pics. They should be slightly countersunk so the tops of the nails are smooth with the playfield.