This work aims to present a navigation scheme whose topmost layer further considers the presence of obstacles and steers the aircraft towards a safe path by altering its navigation references. The complete framework is divided into two control layers carrying out the orientation and navigation, while a third obstacle-aware layer, which is based on a Virtual Leader-Follower coordination problem, generates the positioning references for the navigation controller. This outline allows designing the inner control layers independently, without obstacle awareness, giving flexibility to different combinations of UAVs and controller laws. To validate the proposed structure, numerical simulations are performed where moving obstacles are considered. In addition, experimental testing is carried out by implementing the three-layer navigation in a quadrotor aircraft, performing an independent trajectory while in the presence of a static obstacle. Both tests show acceptable results, and the obstacle collision avoidance is reached.