The focused ion beam scanning electron microscope system combines the advantages of scanning electron microscope and focused ion beam system.Based on the advantages of high resolution，in-situ processing and observation, its applications in defect anatomical analysis, pixel anatomical analysis, transmission electron microscope sample preparation and circuit repair are studied in this paper. The method of locating pixels with problems and the specific process of circuit repair are introduced in detail, and its important role in the development of infrared focal plane detectors is illustrated.The system is an indispensable characterization means in the development of high-performance infrared detectors.