A high-resolution shadow mask, a nanostencil, is widely used for high resolution lithography. This high-resolution shadowmask is often fabricated by a combination of MEMS processes and focused ion beam (FIB) milling. In this study, FIB milling on 500-nm-thin SiN membrane was tested and characterized. 500 nm thick and $2{ imes}2$ mm large membranes were made on a silicon wafer by micro-fabrication processes of LPCVD, photolithography, ICP etching and bulk silicon etching. A subsequent FIB milling enabled local membrane thinning and aperture making into the thinned silicon nitride membrane. Due to the high resolution of the FIB milling process, nanoscale apertures down to 60 nm could be made into the membrane. The nanostencil could be used for nanoscale patterning by local deposition through the apertures.