The process model is very essential for the model based control design. The model of the process can be identified using system identification algorithm. The system identification is done through the open loop and closed loop approaches. In this work, the lab scale conical tank setup configured as a non square MIMO system. The conical tank system is identified through the both appraoches, the effectiveness and need of the both approaces are discussed. Based on the open loop identified model the controller designed and the controller implemented in the real time the to record the process data. From this data the closed loop identification are conducted uisng N4SID algorithm. The controller seetings are obtained using the smith predcitor based IMC based PI controller for the obtained model. The proposed identification algorithm and controller tuning show the better reults over the conventional method. Moreover, this method is applicable for all the non square MIMO system.