An apparatus and a method to remove a resonance frequency of a system in which an unnecessary resonance frequency occurs in a head stack assembly (HSA) having a head for reading/writing data. The HSA is identified and filtered to prevent mechanical damage caused by resonance. The system is artificially excited to identify a potential resonance frequency of the system. The system is designed so that the identified resonance frequency is filtered. Thus, resonance frequency components outside of Nyquist frequency bandwidth of the system can also be identified. Also, the resonance frequency can very easily be identified in a time domain without a complicated calculation process such as an additional frequency transformation process. Coefficients of a programmable filter are updated using the identified resonance frequency to prevent mechanical damage caused by resonance and improve a servo tracking performance and reliability of data.