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An experimental approach for modeling and identification of two tank system was considered. For the system that we considered modeling has been carried out with theoretical values. The practically obtained values from series of experiments the used to correlate the simulated values, the process we have considered is the MIMO process which is difficult being the interaction exists, the interactions can be eliminated for better control action using the existing the methods. Simulations with MATLAB has been carried out and the simulated results are used in the real time experimental set using LAB VIEW. There is great degree of the Accuracy between the estimated values and simulated which can be practically demonstrated with the experimental setup. In this relay feedback approach is being considered for conducting the autocuing test to estimate the parameters.