Total Annihilation map making programs like Annihilator use SCT files as definitions of "pieces" of a potential map. Some pieces may be an island, others open water, or just a hill. When making a map, the map making application provides a list of all available "sections" (SCT = section), which are then placed by the map maker into some sort of final playable map.
SCT files are almost exactly the same as a TNT file, but on a much smaller scale and contain fewer specifics like water height.
For people wanting an in-depth specification of the actual file format, you can view this document: