An applied bias voltage between the atomic force microscope tip and the substrate is one of the important factors related to the growth of oxide patterns. A pulse modulator was used to apply a pulsed bias voltage that synchronizes with the resonance frequency of the cantilever between the tip and the substrate in tapping mode. The height of the protruded oxide structure was increased for short duration times of the pulsed bias due to the reduction of built-up space charge in oxide. The aspect ratio of patterns using pulsed bias voltage was about two times higher than that using continuous bias voltage. This study revealed that the pulsed bias has an advantage for obtaining a higher aspect ratio pattern than the continuous bias by reducing the effect of space charge in oxide.