You have at least four options with a damaged non-hex filter boss. Normally, there is a special tool to remove them, but I use a 3/4" nut split lengthwise, that I clamp (Vice Grips) really firmly to screw them out and in. See below.
If you can't get the split nut on due to the damage, option two is to weld a nut to the boss to get it out and use the split nut to install a new one from the Ford parts counter, machine shop, or the boneyard.
Option three is to hack a screwdriver slot in the end of the boss and use a fashioned tool (chisel, scrap metal piece, etc.) to remove it.
Option four is to use a large 'easy-out' or equivalent on the inside surface, such as a cold chisel or an actual broken screw extractor, that can be driven-in to get a bite, and then wrenched out.
If you're lucky, the new one will be the hex type and can be installed without fuss. It's odd the machinist didn't fix that issue, as they should be removed during the rebuild to clean the passages thoroughly.