Research has presented several approaches to achieve varying degrees of fault-tolerance in unmanned aircraft. Approaches in reconfigurable flight control are generally divided into two categories: those which incorporate multiple non-adaptive controllers and switch between them based on the output of a fault detection and identification element and those that employ a single adaptive controller capable of compensating for a variety of fault modes. Regardless of the approach for reconfigurable flight control, certain fault modes dictate system restructuring in order to prevent a catastrophic failure. System restructuring enables active control of actuation not employed by the nominal system to recover controllability of the aircraft. After system restructuring, continued operation requires the generation of flight paths that adhere to an altered flight envelope. The control architecture developed in this research employs a multi-tiered hierarchy to allow unmanned aircraft to generate and track safe flight paths despite the occurrence of potentially catastrophic faults. The hierarchical architecture increases the level of autonomy of the system by integrating five functionalities with the baseline system: fault detection and identification, active system restructuring, reconfigurable flight control, reconfigurable path planning, and mission adaptation. Fault detection and identification algorithms continually monitor aircraft performance and issue fault declarations. When the severity of a fault exceeds the capability of the baseline flight controller, active system restructuring expands the controllability of the aircraft using unconventional control strategies not exploited by the baseline controller. Each of the reconfigurable flight controllers and the baseline controller employ a proven adaptive neural network control strategy. A reconfigurable path planner employs an adaptive model of the vehicle to re-shape the desired flight path. Generation of the revised flight path is posed as a linear program constrained by the response of the degraded system. Finally, a mission adaptation component estimates limitations on the closed-loop performance of the aircraft and adjusts the aircraft mission accordingly. A combination of simulation and flight test results using two unmanned helicopters validates the utility of the hierarchical architecture.