The present invention relates to a missile or munition with a hierarchical, modular, closed-loop flow control system, more particularly to aircraft or munition with flow control system for enhanced aerodynamic control, maneuverability and stabilization. The present invention further relates to a method of operating the flow control system.Various embodiments of the flow control system involve elements including flow sensors, active flow control devices or activatable flow effectors, and logic devices with closed loop control architecture. The sensors are used to estimate or determine flow conditions on the surfaces of a missile or munition. The active flow control device or activatable flow effectors create on-demand flow disturbances, preferably micro-disturbances, at different points along the various aerodynamic surfaces of the missile or aircraft to achieve a desired stabilization or maneuverability effect. The logic devices are embedded with a hierarchical control structure allowing for rapid, real-time control at the flow surface.