I can't believe no one has said this already!
Get rid of it manually, one bubble at a time. Cut your pumps off. If you have ridgid tubing great, but I don't. You just connect the ridgid tubing to standard .225" tubing (airline tubing) or just use the airline tubing to carefully break the bubble algae off the rock. It has a "root" and there is a way to break it off and get the whole thing, just go at it from the side. I should mention that all this is being done while you are siphoning water through the tube, effectively sucking out the bubble algae. With the pumps turned off, there is little water movement, and if you happen to pop one, you just hover over it and around it, effectively siphoning out all the spores that would be released and sprad all around the tank if the pumps were on. Chances are, with this method alone, it will come back. That is why you keep emerald crab(s) to finish the job, effectively removing and eating the leftover "root"
Did I mention how effective this method is?
Edit: BTW my emerald crab is not the slightest bit green, its not a greenish grey, it is just grey, and it destroys bubble algae. If you can get a grey one try that.