The present invention provides a system and method for actively manipulating and controlling aerodynamic or hydrodynamic flow field vortices within a fluid flow over a surface using micro-jet arrays. The system and method for actively manipulating and controlling the inception point, size and trajectory of flow field vortices within the fluid flow places micro-jet arrays on surfaces bounding the fluid flow. These micro-jet arrays are then actively manipulated to control the flow behavior of the ducted fluid flow, influence the inception point and trajectory of flow field vortices within the fluid flow, and reduce flow separation within the primary fluid flow.