I have just bought a second-hand mountain bike and the rear wheel is made of alloy and has small rust flecks/spots on it. Any advice on how to clean? I cleaned the rust off the forks with a small wire brush (used for cleaning spark plugs on my car) and an anti-oxidant. Would this work on the wheels? I am worried about scratching the alloy.
If it's truly an alloy rim, it isn't rust. Use a metal polish, like you find at the auto parts store for polishing alloy wheels.
It will clean of and smooth out any surface issues without removing to much material.
It takes elbow grease, or you can use a Dremel with a jewelry polishing wheel on it to do it faster.
Use steel wool, or preferably brass wool. Both will take out flecks and rust. The benefit of brass wool is that any left on the wheel will not rust.