FIB is currently the economic methods to produce nano-structure below 100nm. In the past, FIB manufactures nano-structure patterns also unsatisfactory. In this study, the influence of twice deposited mask layer on the aspect ratio of nano-structure and verticality of side wall contour was discussed. The single mask layer is used for pattern transfer. Pattern distortion may occur during etching due to several factors like improper parameter setting, limitation of machine table, etc. The most common situations are aciculate and salient shape on the top and angle of slope which is too big to be vertical. In order to improve above-mentioned situations, a mask layer of multi-deposition was designed to protect the side wall so that it could retard etching. In addition to modifying verticality of side wall, the aspect ratio could be raised indirectly because the second deposition had reduced the interval between patterns. In the aspect of using machine table, the first mask layer, chromium, which was deposited by the sputtering machine. And the etching pattern was directly written on the first mask layer by focused ion beam. The silicon was uncovered at etched place, and then the second mask layer, silica (SiO2), which was deposited by the sputtering machine. The surface contour was directly covered with silica layer. Right after that, the top and bottom of silica were removed through vertical etching by inductively coupled plasma machine. The silica on the side wall of structure was retained to protect the side wall and raise aspect ratio. Eventually, the silicon was etched by the same way of inductively coupled plasma machine that it was researched on the difference in etching gas. And there was a comparison between chlorine and fluorine gases. After optimizing parameters, the nano-structure was made under 100nm.