Focused Ion Beam(FIB) systems is a useful tool for the fabrication of micro-nano scale structures. In this study, the effects of FIB etching on the Au microstructure are systematically investigated. As the fabrication parameters, ion dose, dwell time and beam overlap ratio are studied. First, the increases of Ga ion dose makes the milling yield higher and the sidewall of milling profile steeper. Dwell time is found to have little effects on the milling profile due to the relatively large milling area of $1 imes1{mu}m^2$ used in this study. However, beam overlap significantly affects not only milling rate but also milling profile. As the beam overlap ratio changes from positive to negative, the development of regular cross-stripe patterns at the bottom with low milling rate is observed.