Older Alembics would have silver dots if the didn't have LEDs. Distillates and Spoiler would have silver or bronze dots that would be under the finish - not much you can DIY on the cleanup there. Newer instruments (maybe 1987 -) would have aluminum side dots or bronze side dots depending on the original order, and are likely not under the finish. To clean these, a light scrubbing with white scotch brite should do the trick. You can also sand a couple of swipes down the edge of the board with a fine grit paper (mind to miss the finish on the side of the neck).
You said *inside* the dots - which may indicate you have LEDs in the bottom of tiny wells. When we used an inlaid strip of wood under the frets for the LEDs, the LEDs were at the bottom of holes drilled in the Ebony. Some people even have LEDs but they don't know because they filled up with gunk over the years before they got the instrument. The newer LEDs have a diffuser that fills up this space and so it's never an issue now.
