The possible mishaps of Unmanned Air Vehicles (UAV) could be significantly reduced by installing powerful Structural Health Monitoring (SHM) systems. In this study the performance of a modal analysis based SHM system was studied by using the Finite Element Method, an experimental setup, and implementation on a simulated UAV with four rotors. The study indicated that the natural frequency and the load carrying capability of structure vary with the significance and location of the defects. The defects close to the fixed end of cantilever beams were easier to detect than the ones close to the free end by monitoring the natural frequency of the structure with the proposed Index Based Reasoner (IBR). Piezoelectric fibers effectively monitored the vibration of the cantilever beams in the experiments.