Candice I haven't tried to drill out the markers on the maple fingerboard necks but DB thinks they are plastic markers.
I'd get a centre punch and mark the centre of the circle best you can and try drilling say a 1.5mm or 2mm drill and confirm if they are plastic or drawn on. If they are drawn on you will need a brad point drill bit the same diameter of your MOP or pau shell markers. I usually have a practice on scrap wood to try get the depth correct and mark the depth with some insualtion tape. Remember they should be glued in a bit proud and sand down level