It is well-known that real non-minimum phase (RNMP) zeros impose a tradeoff between the settling time and undershoot in the step response of flexible systems. Existing methods to alleviate this tradeoff predominantly rely on various advanced control strategies without delving into a broader mechatronic approach that combines physical system and control system design. To address this gap, this paper proposes a proportional viscous damping-based physical system design in combination with feedback control and prefilter design. First, the effect of proportional viscous damping on RNMP zeros of flexible systems is established to propose a damping strategy that pushes all the RNMP zeros further away from the imaginary axis. Then, a step-by-step mechatronic system design process is presented to apply this damping strategy along with full state feedback control strategy and prefilter to a multi-DoF flexible system. The application of this design process yields simultaneous improvement in the settling time and undershoot in the step response of this flexible system.