In this paper a novel hierarchical motion control scheme for quadrotor aerial vehicles equipped with a manipulator is proposed. The controller is organized into two layers: in the top layer, an inverse kinematics algorithm computes the motion references for the actuated variables; in the bottom layer, a motion control algorithm is in charge of tracking the motion references computed by the top layer. A simulation case study is developed to demonstrate the effectiveness of the approach in the presence of disturbances and unmodeled dynamics.