The role of irreversible electroporation using pulsed electric field is to generate high-voltage (HV) pulses with a predefined magnitude and duration. These HV pulses are applied to the treatment chamber until decontamination of the sample is completed. In this paper, a new topology for HV rectangular pulse generation for water disinfection applications is introduced. The proposed topology has four arms comprised of series-connected half bridge modular multilevel converter cells. The rectangular pulse characteristics can be controlled via the software controller without any physical changes in power topology. The converter is capable of generating both bipolar and monopolar HV pulses with microsecond pulse durations at high a frequency rate with different characteristics. Hence, the proposed topology provides flexibility by software control, along with hardware modularity, scalability, and redundancy. Moreover, a cell's capacitance is relatively small, which drastically reduces the converter footprint. The adopted charging and discharging process of the cell capacitors in this topology eliminate the need of any voltage measurements or complex control for cell-capacitors voltage balance. Consequently, continuity of converter operation is assured under cell malfunction. In this paper, analysis and cell-capacitor sizing of the proposed topology are detailed. Converter operation is verified using MATLAB/Simulink simulation and scaled experimentation.