Good luck.
1) Best I have heard if to slowly and methodically pick them off without breaking them.
2) I have also heard of using airline tubing to syphen them out (in this case you can break the bubbles as the spores will be syphened out).
3) Mithrax crabs, if you are lucky, will eat the smaller bubbles (once you get the population under control).
4) There is also a fish, I can't remember which one right now, that will eat the bubble algae. Someone will chime in.
I hope you can beat it. I am slowly trying to conquer this beast myself.