there are some things that may eat it, but it's hit or miss. i have emerald crabs that eat it once in a while.
manual removal seems to be the most effective.
take a siphon hose and start the siphon in a bucket, hold the hose over the bubble algae you are going to pluck off of the rock, then pluck it off. if you pop the bubble in the process, any spores should be sucked up in the siphon.
I sympathize with you. I am fighting bubble algae in my newly purchased reef (it was already eatablished and had a large amount of it). Like Mr X said, so far I have had the best results with removing the algae by hand. I have a few emerald crabs that do graze on it a little, but it does not seem to be their preferred food. I also have a yellow tang that has done a fair amount of eating on it, but I am told that this is extremely rare for the species.
E
Like everyone else, manual removal and water changes. One thing I do is suck the insides out with a syringe and then pick off the shell. Works great if you can have access to syringes and a large bore needle.