Multi-level inverter are preferred choice for PV system applications for past decade because of its better harmonic profile and low dv/dt. Along with these advantage it suffers from power balancing issues which are caused by uneven partial shading. This paper proposes a technique to minimize the difference in discharge levels of upper and lower battery banks. The proposed topology involves selection of isolated panels through optimization by considering irregularity of roof top and worst case conditions. In addition, a control strategy is developed for switching isolated panels depending on difference in discharge levels. This topology makes the system to run longtime by complete utilization of battery banks. The proposed topology is verified using three level topology using cascaded bridge configuration accompanied by two battery banks in MATLAB/SIMULINK environment. © 2014 IEEE.