System and method for applying mask data patterns to substrate in a lithography manufacturing process are disclosed. In one embodiment, the method includes providing a parallel imaging writer system, where the parallel imaging writer system includes a plurality of multiple charged-particle beam (MCB) imaging units arranged in one or more parallel arrays, receiving a mask data pattern to be written to a substrate, processing the mask data pattern to form a plurality of partitioned mask data patterns corresponding to different areas of the substrate, identifying one or more objects in an area of the substrate to be imaged by corresponding MCB imaging units, and performing multiple exposures to image the one or more objects in the area of the substrate by controlling the plurality of MCB imaging units to write the plurality of partitioned mask data patterns in parallel.