A numerical code unique to each Starfleet vessel that lets one ship take remote control of another's systems, intended to stop a captured ship being used against the Federation.
The prefix code is explained in Star Trek II: The Wrath of Khan. Khan Noonien Singh, having seized the USS Reliant, cripples the unprepared Enterprise in a surprise attack and demands the data on Project Genesis.
Kirk stalls for time and has Spock call up the Reliant's code on the command console. Every ship has its own combination, held on file aboard other Starfleet vessels. With it Kirk transmits an order that drops the Reliant's shields, and the Enterprise fires what weapons it has left into the unprotected ship.
Khan, unfamiliar with the vessel, cannot find the override in time and has to withdraw. The delay buys the damaged Enterprise the time it needs to limp away.