Recently, H-bridge pulse width modulation (PWM) micro-stepping motor drivers have been widely used for 3-D printers, robots, and medical instruments. Differently from a simple PWM motor driver circuit, the H-bridge PWM micro-stepping motor driver circuit can generate radio frequency (RF) electromagnetic interference (EMI) noises of up to several hundred MHz frequencies, due to digital interface circuits and a high-performance CPU. For medical instrument systems, the minimization of EMI noises can assure operating safety and greatly reduce the chance of malfunction between instruments. This work proposes a passive-filter configuration-based circuit design for reducing up-to-several-hundred-MHz EMI noises generated from the H-bridge PWM micro-stepping motor driver circuit. More specifically, the proposed RF EMI reduction approach consists of proper passive filter design, shielding in motor wires, and common ground design in the print circuit board. The proposed passive filter configuration design is validated through the overall reduction of EMI noises at RF band. Finally, the proposed EMI reduction approach is tested experientially through a prototype and about 16 dB average reduction of RF EMI noises is demonstrated.