This small PLA block has a hole on one side (not shown in picture) that allows a standard M5 bolt to pass through. Make sure you print this with the hole facing up and with proper post-processing gcode to pause your print so you can insert the nut.

Every test I have done hasn't had any issue with extruding plastic on top of the nut but you may encounter adhesion issues, this is mainly due to printers printing the inner circle before the infill. Try experimenting with glue or plastic nuts if this becomes a problem.