is he the only one in the tank still? what are you treating him for? If it where me and there was concern for further stress I would: Make sure the net is the right size. Remove any rocks or plants that can topple over and cause dammage. Also remove any caves or decor that will get it the way. Turn all lights down to a minimum about 1/2 hour before you net him. Slowly approach the aquarium and slide the net in the opposite side of the tank of the fish. Slowly approach the fish with the net. When oppurtunity arrises to make a swipe at him go for it. This is how I net my "scaredy cat" fish. My Oto's (not scared cats) and betta will swim in the net out of curiousity. Add a little salt (sodium chloride, epsom salt or potassium chloride) to the treatment water or melafix to help heal any slime coat loss from the net or stress. Hope this helps.

you can treat him in the tank hes in allready. why stress him anymore
if what he has is contagious then the other fish could get it as well.
is this a flesh wound from fighting? most flesh wounds heal on their own. i have central american cichlids and sometimes they fight pretty bad. the only time i remove one is if hes in really bad shape and needs to recuperate. ill add anitbiotics only if needed. usually after 2 weeks in a tank to himself with plenty of food he is ready to go back to the fighting ring lol
but for me the best way to net fish has been with 2 nets. chase him with one and grab him with the other, cornering is the best bet with the second net to the top of the tank this way when he swims up you can grab him. the bigger the nets the better, small nets are a joke. get a 12" net (2 of them)
id like more info on why he needs to be moved though and treated seperately