I luckily have not had this problem, but I just found this on the web as a possible solution:
"The straw method. I have come up with my own method. It appears to be the safest and surest way to remove the aptasia. The cost is that of a stick of Two Little Fishy epoxy and a clear straw. You can go to McDonald's or Burger King and buy a shake to get one of these high tech straws. I came to this method because every time I tried to plug an aptasia in a hole it would find a new hole to peek out of. Here is the procedure. Cut a piece of straw to about 1 inch. Use the epoxy putty to stick the straw onto where the aptasia is peeking out of. This will eventually lead the anemone out of the rock and into the straw to peek its tentacles out to capture food and light. Once you see the anemone has moved out of the rock and into the straw tunnel, remove the straw with the anemone in it. Safe and effective. At least I have good results using this method. "
Here is the link where this information came: http://www.mn-aquarium.org/masart60.htm
Hope that helps!
Regards,
Frank