I have some red bubble algae and I have found that cutting a point into a piece of plastic hose and using it to punture the bubble and then suck the spores up with it works great.
When I do my weekly water change, I just start siphoning out the water and then puncture the bubbles and suck the crud out.
Afterwards, I use tweezers to pick off what is left of the deflated bubble.
I am slowly winning the war and one day I won't have to do this anymore.