You can't just leave it, it's at least 1/8" deep and it will have a center point in the middle usually from the bit. To remove them you can completely drill them out with an equal sized forstner drill bit. But usually I will take a smaller drill bit, maybe 1/8" and drill until I can feel I poked through it. Then usually a little wiggle on the drill bit will pop it loose, depending on the guitar. I wouldn't try that on pearl or abalone, just plastic. (Your squire has plastic) I assume it's a Rosewood fretboard, in which case you can fill with a dark wood filler, or replace them with black dots, which will seem to disappear. You can also cut plugs (with a special bit) from matching Rosewood, or you can mix Rosewood dust with epoxy for a custom paste filler with a short work time.