A method of wafer repairing comprises identifying locations and patterns of defective regions in a semiconductor wafer; communicating the locations and patterns of defective regions to a direct-writing tool; forming a photoresist layer on the semiconductor wafer; locally exposing the photoresist layer within the defective regions using an energy beam; developing the photoresist layer on the semiconductor wafer; and wafer-processing the semiconductor wafer under the photoresist layer after exposing and developing.