A composite charged particle beam apparatus comprises an FIB column and an SEM column arranged so that the ion and the electron beam irradition axes intersect with each other substantially at a right angle. A sample stage mounts a sample, and a detector detects secondary particles generated from the sample when irradiated with the ion beam or the electron beam. An observation image formation portion forms an FIB image and an SEM image based on a detection signal of the detector. An optical microscope observes the sample, and a display portion displays the FIB image, the SEM image and an optical microscope image. A stage control portion changes the coordinate system of the sample stage to any selected one of the coordinate systems of the FIB image, the SEM image and the optical microscope image.