There is not a 100% guaranteed method that will work. Shrooms tear really easily. Some will come of easily, and some will fight to the death. Even if you can peel them off, they don't seem to hold where you want them to and will roll around on the sandbed.
The only way I am able to reliably remove some of those "holding till the death" was to take the rock out of the water, place on a wet towel on a work bench, and use a flat screwdriver as a chisel and try to chip of the rock just underneath them. For a pea sized shroom, just chip off a pea sized rock underneath them. Then you can use CA to glue that wherever you like. Granted, you may tear some because the type of rock they are holding on to can vary greatly, but you'll get better after practicing. That said, practice a bit first!
Alternatively, you could always try scrubbing the rock with a stainless steel brush (looks like a metal bristled tooth brush that can be had at a local welding supply store), and scrub the algae off. So long as your phosphates are low it shouldn't grow back too fast.
Hope that helps?
Jeff