Diesel automotive engines after-treatment systems face greater challenges with every iteration of emission norm legislation. Major improvements in tailpipe NOx removal need to be achieved to fulfil the upcoming post EURO 6 norms and Real Driving Emissions (RDE) limits. Multi-brick systems employing combinations of multiple selective reduction catalysts (SCR) with an ammonia oxidizer (CUC) are proposed to cover operation over wide temperature range, however, control of multi-brick systems is complex due to many unmeasurable states. Usage of sophisticated model based predictive controls (MPC) makes the control task straight forward and less error prone compared to classic PID control. This paper shows the application of MPC to a SCR multi-brick system. Storage levels for SCR are calculated by optimization based on NOx conversion efficiency keeping tailpipe NH3 slip under emission limits. Two MPC controllers are used to achieve the best possible performance of the multi-brick SCR system. A low level MPC computes the optimal urea dosing based on desired ammonia storage for given operating condition while respecting NH3 slip constraint over the prediction horizon. A high level, or supervisory, MPC controller computes the optimal storage set-point based on NOx conversion efficiency required and accounting for system parameter change, for example, catalyst aging. Unmeasurable states of the system are estimated by an Extended Kalman Filter (EKF). The entire control system was integrated into a prototyping ECU. The control is real time capable and feasible for mass production. The use of a systematic design toolchain based on LMS Amesim and OnRAMP design suite allows flexible changes in the system architecture and speeds up the whole development process.