Raptor Nails - plastic nails for work holding

[Zman (MICHAEL ZEMANEK)]

Did a search on the Forum. This was one of the first.

Flattening Waste board with brad nails remains

Most folks who use a nailer for workholding use polymer nails so as to avoid this difficulty. MDF is cheap compared to an endmill, my inclination would be to replace it — buy a suitable piece, pull the current wasteboard, clamp together, use transfer punches, countersinks and drills to remake the needed holes.