Deep scans are different from a normal scan; they'll uncover materials they lie deeper underground where normal scans couldn't detect.
In order to be able to deep scan areas, you'll first need to research the Adapted Probes technology under the Physics tree. Once you have this technology researched, it's then simply a case of deep scanning every sector of the map.
To earn this achievement quicker, make sure you select the Fast Scanning rule under the Game Rules before you start your game as this will scan sector's ten times faster.