A significant obstacle to the implementation of autonomously-controlled aircraft into the national airspace system is the tendency of autonomous systems to operate in non-deterministic manners. While autonomous aircraft may have the capability to safely maneuver in shared airspace, they often do not operate under the same flight guidelines as a trained human pilot, leading to potential misinterpretation of actions and flight paths. The Autonomous Formation Flying System (AFFS) provides both autonomous control for formation flight as well as a deterministic solution for changes in trajectory. The AFFS gives rotorcraft the capability to autonomously avoid multiple static or moving obstacles, including pop-up threats, while flying in formation. It functions in dynamic three-dimensional situations with both small and large heterogeneous formations, facilitating safe and efficient entries into and exits from a formation while also allowing seamless, real-time changes in the formation structure and following the standard "rules of the road" adhered to by trained human pilots. The testing of this innovative system included a series of manned and unmanned multi-ship simulations as well as flight-test experiments in which Georgia Tech's GTMax rotorcraft UAV was flown in formation with a manned high-fidelity UH-60 simulation. Both the simulations and flight-tests effectively demonstrated the autonomous formation flying and collision avoidance capabilities of the AFFS.