In this paper, we discuss the process of integrating an Autopilot with Unmanned Aerial Vehicle sensors and actuators to perform full Autonomous mission. Unmanned aerial vehicles (UAVs) play an important role in the current military operations in the recent years with its great advantages for autonomous flying capability that provides much less manpower, cost and less risk to human lives. Also there are many potential applications for UAVs in civilian environment like photography, agriculture planning and many others. To gain an autonomous flying requires many flight testing and evaluations to decide to use certain airframe aircraft integrated with the autopilot in a required application. Using a low cost Autopilot, a MATLAB program was written in order to analyze log files for every flight test in different SUAV modes (Manual, Stabilize and Auto). Tuning the autopilot PID control gains during flight testing has a significant effect on aircraft flight stability that requires less iteration until it reaches an adequate value which requires an intensive work.