The application of focused ion beam(FIB) technology has been broadened in the fabrication of nanoscale regime. The extended application of FIB is dependent on complicated reciprocal relation of operating parameters. It is necessary for successful and efficient modifications on the surface of silicon substrate. The primary effect by Gaussian beam intensity is significantly shown from various aperture size, accelerating voltage, and beam current. Also, the secondary effect of other process factors - dwell time, pixel interval, scan mode, and pattern size has affected to etching results. For the process analysis, influence of the secondary factors on FIB micromilling process is examined with respect to sputtering depth during the milling process in silicon material. The results are analyzed by the ratio of signal to noise obtained using design of experiment in each parameter.