A new tool of surface patterning technique for general purpose lithography was developed based on shadow mask method. This paper describes the fabrication of a new type of miniaturized shadow mask. The shadow mask is fabricated by photolithography and etching of 100-mm full wafer. The fabricated shadow mask has over 388 membranes with apertures of micrometer length scale ranging from 1 μm to 100s μm made on each 2mm x 2mm large low stress silicon nitride membrane. It allows micro scale patterns to be directly deposited on substrate surface through apertures of the membrane. This shadow mask method has much wider choice of deposit materials, and can be applied to wider class of surfaces including chemical functional layer, MEMS/NEMS surfaces, and biosensors.