Years ago, I would have cut off the nubs or shaved the base with a hobby knife, occasionally breaking off a figure from the base, and probably nicking myself with the blade occasionally. A tedious and precise business in any event.
Now, I use a tungsten-carbide grit file made by Perma-Grit Tools. I've mentioned these a few times before, but they are one of the most useful hobby tools that I've found. They last forever; I've only replaced one in over 25 years of use, and that was because I gummed it up severely, not because the grit wore off.
Anyway, here are couple of pics of the nubs that I'm cleaning off of the infantry and of the Perma-Grit tools.
You can see the nubs on these H&R 6mm Modern Soviets
above. The nubs are most visible on the underside of
the base on the middle figure, laying on its back.
Some of my Perma-Grit files. The angled
one the left is probably the one I use the most.
For this task, I mostly use the Fine Angle File. Several of my files have both fine and coarse grit sections, but I don't think those are available anymore. The fine grit attacks soft metals quickly, while the coarse grit makes shaping plastic like styrene a piece of cake, and both grits work well for various tasks associated with resin.
Sorry for the commercial, I'm don't own the company, nor sell the product, I'm just a happy customer.