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This paper investigates a factorization approach to sensitivity loop shaping for disturbance rejection in hard disk drives (HDDs). The advantage of the factorization approach is that the system sensitivity function can be expressed explicitly in terms of a unique design parameter. This greatly simplifies the control design process to make the system sensitivity function match a chosen target sensitivity function with guaranteed stability. By decomposing the controller structure, the design parameter is revealed to behave as a plug-in disturbance filter, the design of which is then presented to suppress the dominant disturbances at some specific frequencies. It is also shown that based on the nominal control system the proposed disturbance filter can reduce the sensitivity gains at specific frequencies without worsening the neighbouring sensitivity gains. Simulation together with implementation results demonstrate that the proposed method can effectively suppress the disturbances around the servo bandwidth and accordingly offers a superior tracking accuracy in comparison with other existing filters.