My ducks, despite being very friendly and enjoying spending time with me, also dislike being handled for bumblefoot treatment. For their own good I just take care of it as quickly as possible. To catch them I gently herd them into a corner and then quickly grab one. This way I avoid chasing them which seems to be the scariest part. Struggling also seems upsetting, so the towel burrito can work very well to secure their wings and keep the chaos down.
Before I catch my duck I have all my supplies ready, that way my duck has to spend as little time stressed out as possible. I even cut my vet wrap first.
Neoprene duck booties overnight worked well for my ducks, too. During the day my ducks splashed water into them so I let them go barefoot.
You might also look at prevention. Some duck feet seem really sensitive to harder surfaces. I've had two ducks that were this way, and one in particular had bumblefoot repeatedly until my vet recommended that I change her environment. Since I did that I haven't had bumblefoot for... It must be 4+years now. I switched to grass only outside, 4-6 inches or straw inside. No wood shavings, boards, rocks, gravel, patios stones, ect. It seems that not all ducks need this, though, and it is a lot of work.