This study demonstrates nano-scale lithography process on localized (100) silicon (p-type) surface using modified AFM apparatuses and controlling methods. AFM-based experimental apparatuses are connected the customized pulse generator that supplies electricity between conductive tip and silicon surface maintaining constant humidity during processes. Then pulse durations are controlled according to various experimental conditions. The pulsed electrochemical reaction within the gap between conductive tip and silicon surface induces the formation of oxide with nano-scale topographies. Various heights and widths of oxides can be created by AFM surface modification according to various pulse durations and applied electrical conditions under humidity environment. In addition, it can be known that oxides are completely removed after sample surface is etched in diluted HF solution, which shows micro/nano-scale grooves can be fabricated after predefined chemical treatment. They are wider than oxides widths and have several nanometer depths. Nano patterning technique from this experiment suggests that pulse electrochemical machining process has bright potential for advancing nano machining technologies.