Controller performance assessment of SISO and MIMO systems requires effective and systematic identification of the associated system models based on closed-loop data. In this work, a new methodology for the identification of the process, controller and disturbance models is presented for the purpose of enabling the evaluation of the performance of MIMO control systems. The methodology is based on subspace identification algorithms for the identification of the controller, process and disturbance models from closed-loop data. However, identification of the process model is enhanced by the estimation of the associated interactor matrix via the Variable Regression Estimation technique, the existence of which is mathematically proved. The proposed identification methodology is applied to two 2 x 2 systems utilizing both step-response and PRBS closed-loop data.