The best way to eliminate Bubble algae is to manually remove what you can via siphon. Then treat with vibrant at recommended dose.
Never pop the bubbles. Found that out the hard way and a veteran reefer on here did too. I was at his house and told him about a bubble algae problem I was having several years ago in a new tank. He said…you can pop the bubbles as long as your nutrients are low. Then proceeded to pop some large bubble algae bubbles in his tank. Several months later he had a massive outbreak like I did. Classic!
BA can be large, small, and tiny. They can get in the overflow box, plumbing, return pumps, wave makers, etc. If you have certain species they can be next to impossible to eradicate.
At that point removing sensitive corals and using Vibrant at a higher more frequent dose might be your only option, because it definitely drops nutrient levels the bigger and more frequent the dose.
Here are some pictures of my outbreak several years ago. Some of these new bubbles were almost microscopic and this species was really aggressive. I have seen a large species in established systems be ok and never get out of control.
Manually removing a problem of this scale below is next to impossible. Vibrant would have been my only solution then. However, Vibrant wasn’t created yet. I had to shut down the system.
Best of luck with your outbreak.