The outcome of highly flexible aircraft requires new approaches in control design. In this research, we apply the loop separation concept, which consists in two control loops. The inner loop is capable of stabilizing the plant of the flexible aircraft, while is holding shape of the trimmed structure. Once the highly flexible aircraft is artificially transformed in a slightly flexible aircraft, the second loop or outer-loop is designed according to conventional, rigid-body-based control. Three control approaches were evaluated in the inner loop: LQG/LTR, LQR with output feedback and a direct integration approach. The direct integration approach with uncoupled gains presented better performance. The outer loops for speed, heading, sideslip angle and altitude were estimated using non-smooth optimization techniques and they are capable of attaining the commanded reference with low control energy and inside the maneuver requirements, while the inner loop is capable of reducing the elastic strains of the wing.