I had a number of patches throughout my reef. I did a large water change, took out each rock that was noticeably affected and scrubbed it with a toothbrush while holding it in a bucket of old water. Holding it under water allowed me to see the bryopsis much better, it didn’t matt to the rock. When the water started getting too green to be an effective rinse, I dumped it and filled another from the tank.
After I had thoroughly cleaned all the infested rock, I took the heater, skimmer, and powerheads to the sink and cleaned them as well. I even had clumps growing on the surface of the sandbed. I removed every bit of the stuff I could see.
I completed the water change, put the rocks and hardware back in, and I haven’t seen any since. That was nearly a year ago.