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In this paper, the design method of a multirate digital filter to handle high frequency resonant modes in hard disk drives (HDDs) or other mechanical actuators is proposed. Instead of using many notch filters, one low-pass filter will handle multiple mechanical resonance modes. The proposed multirate digital filter has robust resonance cancellation capability with comparable or even lower phase loss than using notch filters. The proposed scheme can well handle the high frequency mechanical resonances in the sense of robustness to variations of resonance frequencies and simplicity to implement in practice. The effectiveness of the proposed method is verified by application to a real HDD servo system.