There is provided a method capable of calibrating a sample stage easily. This method is for use in a charged particle beam system having the sample stage for moving a sample and an imaging subsystem for capturing a charged particle beam image and obtaining a final image. The method includes the steps of obtaining the final image from the imaging subsystem (step S100), obtaining correlation information that associates a given position in the final image with a position of the sample stage assumed when the final image was taken (step S102), obtaining length information about a length per pixel of the final image at a final magnification (step S106), and finding a correction between coordinates of the final image and coordinates of the sample stage on the basis of the correlation information and of the length information (step S110).