tf system identification toolbox

I have 3 inputs and 2 outputs on my system ,the tool box gives me an estimation of transfer funtion but it gives like 6 transfer function two for each input with the two outpts.I want it as one transfer function with multiple inputs and multiple outputs to use it in controll system.

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That sounds surprising. Can you post some code so we can see how you are identifying the model(s)?
A single transfer function can only relate a single input and a single output. For a 2 output and 3 input system, you will get a 2x3 matrix with 6 transfer function. So, the MATLAB output is correct. How to use this result depends on what you are trying to do next.

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