Over the last year I've found 3 of them in my tank, here's how I KILL them and they never come back.
I have a small container of Kalk and some Q-Tips, wet the Q-Tip with tank water and then get just a tiny bit of Kalk on the tip of the Q-Tip, take the infested rock out of the tank and then just press the kalk into the aptasia's little area, don't worry if he withdraws and you can't see him, just get the kalk in the right area, let it set for a minute and then use the other end of the Q-Tip to wipe up any excess kalk, you can also use a squirt of tank water over a sink to rinse the remaining kalk off.
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If you can't get the rockout of the water, then still use the Q-tip and do the same procedure underwater, you use such a small amount of kalk that it doesn't cause problems. I had one that was under the encrusting rim of a GSP and I just dabbed the whole are, even got some of the klak on the GSP and didn't cause any problems.