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The increased utilization of flexible structure systems, such as flexible manipulators and flexible aircraft in various applications, has been motivated by the requirements of industrial automation in recent years. Robust optimal control of flexible structures with active feedback techniques requires accurate models of the base structure, and knowledge of uncertainties of these models. Such information may not be easy to acquire for certain systems. An adaptive Neuro-Fuzzy inference Systems (ANFIS) use the learning ability of neural networks to adjust the membership function parameters in a fuzzy inference system. Hence, modelling using ANFIS is preferred in such applications. This paper discusses modelling of a nonlinear flexible system namely a twin rotor multi-input multi-output system using ANFIS techniques. Pitch and yaw motions are modelled and tested by model validation techniques. The obtained results indicate that ANFIS modelling is powerful to facilitate modelling of complex systems associated with nonlinearity and uncertainty.