Removing Fret Markers

I suppose you could drill them out on a drill press and plug the holes with wood plugs of the same type, color and grain width as you fingerboard. Then replane the board. They would most likely still show.

If you tried to fill them with some type of hardening filler, you'd almost certainly end up with them bowled in. Even if you got the shape right, they'd stick out like a sore thumb in anything but a very dark, tight-grained wood like ebony.

 

I knocked mine out with thumb tacks. I gently hammered the tip of the tack far enough into the center of the dot to gain leverage and plopped them out. Some broke but it is easy to clean it out. I then filled the dots with superglue several times. Looks great on a rosewood board. Only two of the dots are flawed with a small bubble; not bad for my first time.

I planed my board afterward, but they look perfectly fine with a little dip.

Yeah, I couldn't stand those dots on my board.

 

Tips?
Take your time. My biggest vice is not waiting long enough.

I used superglue because it worked great when I converted the neck to a fretless. When more than a few feet away the board looks completely uniform. Its transparency gives it the same color as the rosewood.