Fabrication of nanopore arrays is of great importance in nanodevices manufacture and basic scientific research. Focused ion beam (FIB) and electron beam lithography (EBL) have been widely used for fabrication of nanostructures.However, it takes very long time to fabricate nanostructure patterns of large area. In this p aper we report a novel fast fabrication method for nanopore arrays of large area by FIB. Each pixel of predesigned BMP file is regarded as a fabrication dot. B y matching the pixel of the presigned BMP pattern with the required fabrication area, nanopore arrays of large area can be fabricated in a very short time.