With respect to the captain jerks, they are quite dangerous. When you remove them, do not try to cut, scrub, scrape, or otherwise mess with them. Just take the loss and throw out the rock they are on. If it’s part of a larger rock, break the rock with a hammer/chisel (outside of the tank), not near the jerks. When you do all this, do it with gloves, safety glasses, no other people or pets around, and preferably outside. Then double or triple bag it and throw it out.
With respect to your question, there are several ways. The easiest I think is to cut a little under them through the rock with bone cutters/coral cutters. Bandsaw also works but is not what I use.