This paper presents vibration reduction control of a voice coil motor (VCM) nano scanner. We had developed a VCM scanner. The scanner has flexure hinges structure. However, the VCM nano scanner has some problems of thermal drift and small damping compared to the PZT driven nano scanner. Especially, the small damping coefficient of the VCM scanner causes mechanical vibration when the control input signal is near to the resonance frequencies. Additionally, disturbance to the VCM scanner and electronic noise in the sensor also cause the mechanical vibration when they are near to the resonant frequencies. The mechanical vibration reduces the servo bandwidth as well as the accuracy, which deteriorates the AFM image of the samples. We design a pre-filter to reduce the signal applied to the VCM nano scanner and electronic noise in the sensor whose frequency is closed the resonant frequency of the VCM nano scanner. We measure the time and frequency response of the VCM scanner without using the pre-filter and with using the pre-filter. Finally, the topology images of a bare wafer are measured and compared using the AFM.