The increased use of FPGAs over the past decade has induced an increased concern about radiation effects, in particular the effects of single event upsets (SEU) in SRAM-based FPGAs. Technology scaling and density increase have caused FPGAs to be more vulnerable to SEU. Therefore, external radiations present an issue not only for space based systems; but also for critical terrestrial applications operating in harsh environment, such as commercial avionics.In order to build robust fault tolerant systems, SEU effects have to be analyzed and modeled so that the designer understands and considers the system's possible faulty behaviors. In this paper, we present a complete automated methodology, based on the use of SEU controller provided by Xilinx, to efficiently emulate SEUs on an FPGA design and extract possible fault models based on radiation effects. The proposed method is applied on a reconfigurable flight control system based on a reference adaptive control model. With the automatic aspect of the proposed methodology, it was possible to emulate a large number of SEUs with reduced time and effort. Experimental results present the design sensitivity, its failure rate as well as its faulty output behavior. Moreover, results analysis disclose the existence of new actuator control fault models that are not considered in fault tolerant systems, these systems being mainly based on the existing well-known models in the literature. The new fault models can be used by the designer at an earlier stage in the design to build robust flight control systems.