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By using an interactive architecture of independently designed guidance and active fault tolerant control systems, this work proposes the development of a novel Guidance and Active Fault Tolerant Control Scheme for a fixed wing Unmanned Aerial Vehicle. As to the guidance segment, an approach, of the Feedback Linearization type, has been exploited for developing, directly on the dynamic model of the fixed wing Unmanned Aerial Vehicle, the guidance system. With reference to the control segment, this paper proposes a novel Active Fault Tolerant Control Scheme based on Adaptive Filters designed by means of the NonLinear Geometric Approach. The aim of these adaptive filters is to provide a fault estimate, which is used in a further control loop, thus avoiding a logic-based switching controller. The simulation results show good tracking capabilities, asymptotic fault accommodation and a stability analysis with respect to perturbed initial condition. Finally a comparison with the performance obtained by using the fault estimate obtained by another method is given.