FND Bases are enemy camps that you can liberate by defeating all the enemies present in the base. The reward will be better if you do not get detected or cause the alarm to be raised. Depending on the base, optional objectives may also be available, such as freeing a hostage, downloading the data, capturing a vehicle, etc. Completing them will result in a better reward for you. Once liberated, bases can serve as fast travel points.
Liberating all FND Bases is required to unlock the "Liberty" achievement / trophy. Other achievements / trophies associated with FND Bases are: "Ninjerilla" (Capture an FND Base without being detected), "Didn't See That Coming!" (Use a Security Control Center to disable all cameras and alarms), and "Co-Dependent" (Capture an FND base with a Co-op partner).