This article presents a Model Predictive Control (MPC) scheme for the Autonomous flight of an unmanned quadrotor. The nonlinear dynamic equations are modeled by a set of Piecewise Affine (PWA) systems, each one for a different operating point of the quadrotor's translational and rotational motions. The proposed control scheme is hierarchical and is consisted by an integral model predictive controller for the translational motions tracking, followed by a model predictive control scheme for the quadrotor's attitude motions' tracking. By the utilization of a PWA realization of the system, the controller is computed for a larger part of the flight envelope of the system. In addition the physical constraints of the system have been also taken into account during the controller design process. Simulation studies are illustrated to prove the efficacy of the proposed control scheme.