Scoop out as much of it as you can mechanically. Do a water change. Use the meds as the per the directions. Scoop out any remnants of bga and do a water change after treatment. If you have a fairly heavily planted tank ( unless you have tons of fish ) I wouldn't worry to much about the benificial bacteria being harmed. Plants can handle small amonia spikes, and you'll be doing a few water changes after treatment anyhow.
