Scanning refers to a Player using their Player Pin to view Thought Fragments of other people around them. Within gameplay, tapping on the black Player Pin in the bottom right hand corner while on the field, 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 Taboo Noise can attack you when you are scanning, even if you do not wish to attack them.
In The Animation, scanning is done when a Player in the UG phases through a person in the RG.
Scanning will return in NEO: The World Ends with You.