A system and method is described for controlling flight trajectories of at least two flying vehicles towards goal positions. The system includes at least two flying vehicles with onboard inertial measurement units for determining and updating orientation, angular velocities, position and linear velocities of the at least two flying vehicles, a motion capture system to detect current position and velocity of each of the at least two flying vehicles, and a base controller in communication with the motion capture system and in communication with the plurality of flying vehicles. The base controller calculates for each of the flying vehicles, at predetermined intervals of time, optimum trajectory paths using piece-wise smooth polynomial functions, applying weighting factors, and enforcing overlap constraints.