If your source material is noisy it can help. Think VHS or captures from a not too good tv reception. Don't expect miracles on cleaning up very poor avi files though. And it will be deadly slow in TMPGenc.

Use the Project Wizard, click on the Noise Reduction, and click on the High Quality. Might want to zoom in and check back and forth enabling and disabling the filter. You should also preview the effect rather than start encoding automatically. See if it is going to do what you intend.