I did not have any 5mm length M3 screws, so I had to add a nut as a spacer to get the right depth. You will need some M3 5mm long screws, and some nuts to drop in when you set the pause in the layer height.

Here is a video of the M3 nuts being inserted at pause point you will need to set. You will need to set pause point just before the top layer of the nuts is printed. It might be different height depending if you print face down or face up, so just scroll through layers to find layer just before it fills the top of the nut holes.