Scanning refers to a Player using their Player Pin to view Thought Fragments of other people around them. Gameplay wise, when you tap on the black pin in the bottom right hand corner while on the district map, it shows the thought fragments of NPCs, and allows Neku and his partner to fight Noise by tapping a Noise symbol.
Usually Noise symbols are not aggressive, and do not attack you automatically. But, there is a black noise symbol which represents a Black Noise known as Taboo Noise. This class of Noise can attack you when you are scanning, even if you do not wish to attack them.