Nanites were machines designed to manipulate matter on the atomic and molecular level.
The nanites created by Genetec Systems were called nanoforms. They could deconstruct objects on a molecular level and then reconstruct them into a new form. They needed to be kept at sub-zero temperatures to remain inactive. (TV: Prisoner of the Judoon)
The Master made a deal with the Tzun to help them invade Earth in exchange for a new body. This was done with nanites that broke down the corrupted Trakenite DNA in his cells and restructured it. The Master was restored to being a "full" Time Lord, allowing him a new regenerative cycle. (PROSE: First Frontier)
The Contagium was a Dalek device. When released into an environment, it transformed its biological host into a factory which produced nanites which burrowed into the brain and placed anyone infected under Dalek control. (COMIC: Fire and Brimstone)