The paper proposes a high precision simulator for the following mode system design in Hard Disk Drives (HDDs). The simulator is composed of two models: one is a precise mechanical plant which includes numerous high frequency vibration modes, and the other is a disturbance signal model which is separated into various disturbances. In the proposed approach, a differential iteration method is applied to identify the precise mechanical plant, providing accurate experimental model analyses. The effectiveness of the synthesized simulator was verified by the comparative studies for experiments and numerical simulations.