Scooping them out by any means should be fine... collect them with your hand, a net, or a cup, and put them in a small container (a specimen jar, stock bag, or anything else) with tank water in it. The part you want to be careful about is to get the water of the new tank as similar to the old tank as possible. If this is a sick fish that will be going into quarantine in a small tank, then fill 50% or more with water from your main tank, and then fill up with fresh, conditioned water as if it was a normal water change. The stress of moving to a new environment, especially for a sick fish, is the riskiest part.
When you get them to the new tank, slowly exchange water in the transport container for water from the quarantine tank. By slowly, I mean 10% at a time. Dip the container into the tank, or pour out some water and pour in some new, so that you get a little bit of tank water each time, and wait a few minutes between each exchange. Its especially important to acclimatize them to the temperature, and try to get the temperature as similar as possible.
Of course, your fish is going to be best in the long term if this QT tank is cycled and properly setup as well.
