Vacuuming the surface of the gravel won't eliminate the parasites, but taking out all organic detritus first helps the medication work against Ich instead of oxidizing organics in the water. So it's good.
Vaccum as you would when doing regular water changes, assuming you do regular water changes. Try to vaccum the entire bottom without removing more than 50% of the water. If you can only do 1/2 one day and 1/2 the next, that's o.k.. If you are treating with medication, it most likely suggests to remove some water and replace with fresh water anyway.
I apologize gaurang for not following the forum very closely latey and so I don't know how familiar you are with equipment so... when we say vaccum, that is not the electrical device used to clean floors with. A gravel vaccum is an open ended plastic cylinder (about 2 inches in diameter and 12 to 24 inches long) attached to tubing (generally 3/4 inch in diameter) that is used like a syphon to suck up gravel and seperate it from gunk (i.e. fish poo and uneaten food) and thereby cleans the gravel. Just wanted to make sure we are on the same page, so to speak. Hope it helps.