Bioscanner

Most Hyperion Federation starships and sensitive areas are equipped with devices that scan one's body using nanobots. Anyone on board is continually scanned. They do this to make sure no spies manage to get onto their ships. Sometimes, they can detect a cloaked spy. However, it is already extremely difficult to get onto a Federation starship as a spy anyway, as the only way to get on most ships are via Teleporters.
Bioscanners function by emitting dense streams of nanobots in a beam-like fashion towards anything that blocks the beams. Most of the time it is people that block the beams as they walk past. These nanobots can record the positions of most of the matter within the target and construct a semi-functional techprint of the entire body to be compared to the one present on the Grand Archive. If they don't match, an alarm is sounded. As these beam emitters are present in a massive number of locations through all HF starships and structures, they are impossible to avoid.
In some cases, it may be possible for an enemy spy to ‘convince’ Federation officers to provide them with information they seek, wether it is via propaganda, threats or whatever method. To counter this method, counter espionage officers are, while at work, always supervised. Civilians do not have acess to data useful for the enemy.