Eye tracking has become a valuable tool to observe and interpret operators' mental state. This may be due to the fact that it is less intrusive than other physiological tools, and also capable of assessing various mental states such as mental fatigue and engagement (e.g. using blink frequency and fixation duration). These states are critical in aeronautical contexts. Therefore, a real-time eye-tracking processing system was developed using eye-tracking glasses worn by the pilot while performing flight and interacting with unmanned aerial vehicles (UAVs). The proposed system is capable of finding areas of interest from different positions, orientations, and distances from a continuously changing field of view. Four computer screens were tracked and in one of them three different areas of interest were defined and tracked in real-time. The goal is to ease the pilot's mental state assessment in ecological settings and ultimately to enhance the pilot-UAVs interaction in Manned-Unmanned Teaming missions.