Get a toothbrush and rubber-band it to the end of your water change hose. Scrub away and the scraps will get sucked up and out of your tank, minimizing the risk of them spreading.
Using a dremel or another rotary tool to chop the rock out from underneath them is probably the best option if you can because then you can sell/trade them
I know your pain - red mushrooms taking over. Just took two rocks full back to the LFS (about 40 shrooms total). For the strays, I find digging beneath the shroom with a flat-bladed screwdriver is the most efficient way to remove the entire shroom. Most reef rock is pretty porous and surprisingly soft.
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