As the technological capabilities of automated systems have increased, the use of unmanned aerial vehicles (UAVs) for traditionally exhausting and dangerous manned missions has become more feasible. The United States Army, Air Force, and Navy have released plans for the increased use of UAVs, but have only recently shown interest in the cyber security aspect of UAVs. As a result, current autopilot systems were not built with cyber security considerations taken into account, and are thus vulnerable to cyber attack. Since UAVs rely heavily on their on-board autopilots to function, it is important to develop an autopilot system that is robust to possible cyber attacks. In order to develop a cyber-secure autopilot architecture, we have run a study on potential cyber threats and vulnerabilities of the current autopilot systems. This study involved a literature review on general cyber attack methods and on networked systems, which we used to identify the possible threats and vulnerabilities of the current autopilot system. We then studied the identified threats and vulnerabilities in order to analyze the post-attack behavior of the autopilot system through simulation. The uses of UAVs are increasing in many applications other than the traditional military use. We describe several example scenarios involving cyber attacks that demonstrate the vulnerabilities of current autopilot systems.