This paper presents an application of fractional order controller for the control of multi input multi output twin rotor aerodynamic system. Dynamics of the considered system are highly nonlinear and there exists a significant cross-coupling between the horizontal and vertical axes (pitch & yaw). In this paper, a fractional order model of twin rotor aerodynamic system is identified using input output data from nonlinear system. Based upon identified fractional order model, a fractional order PID controller is designed to control the angular position of level bar of twin rotor aerodynamic system. The parameters of controller are tuned using Nelder-Mead optimization and compared with particle swarm optimization techniques. Simulation results on the nonlinear model show a significant improvement in the performance of fractional order PID controller as compared to a classical PID controller.