In this paper, we present a hierarchical controller for autonomous aerial vehicles control and navigation. For autonomous rotorcraft flight, it is common to separate the flight control problem into an inner loop that controls attitude and an outer loop that controls the translational trajectory of the rotorcraft. The resulted nonlinear controller is thus, easy to implement and to tune. Furthermore, satisfactory results have been reported in the literature and various navigational tasks have been achieved using this hierarchical control technique. However, this control scheme suffers from the lack of the stability proof and analysis for/of the closed-loop system. Here, we propose a 3D flight controller which is based on the inner- and outer-loop control scheme, and we prove the asymptotic stability property for the connected closed-loop system.