I would be hesitant to remove the parasite while in the water lest it get dropped back into the tank, but if you feel more comfortable doing it while the fish is underwater then perform the "surgery" with the fish held in the Q-tank.
Here is an article copied from guppyplace.tripod.com on how to administer a salt bath in a quarrantine tank:
Salt Treatment/Salt Bath
This is a treatment that is as old as the aquarium hobby itself. Treating with salt is undoubtedly the safest way to treat fishes. While chemicals such as Formalin, Malachite Green, and copper are considered by some to be more reliable, these are strong substances to impose on a guppy and must be handled with care since they have the potential to cause cancer in humans. Using salt is especially handy with guppies, since they are built to withstand a lot of salt - they do that quite well. Salt is especially effective against fungal infections and some parasitic problems such as ich. If diagnosis is difficult, try salt. Normally the salt treatment lasts 10 days. Note: This bath is not intended as an additional treatment and should not be combined with other medication.
bath
Days 1 - 3: add I teaspoon of salt per gallon of water, every morning and every night. (2 teaspoons /gallon/day)
Days 4 - 7: Leave water alone.
Days 8 - 10: Remove half of the tank water each day and replace with unsalted, chlorine-free water at the correct temperature.
If by day 7 you see any improvement (but not a total cure), wait until day 10 to start changing the water in the tank. Be sure to change half the water once a day, for three days at the end of the salt treatment. Also, don't wait longer than 10 days to start changing the water, as the salt itself can begin to cause problems for your fish.