1. A method of calibrating a sample stage in a charged particle beam system having an imaging subsystem for capturing a charged particle beam image and obtaining a final image that can be directly viewed on a display having a given pixel size or recorded as well as the sample stage for moving a sample, said method comprising the steps of: obtaining the final image from the imaging subsystem; obtaining correlation information that associates a given position in the final image with a position of the sample stage as defined by the two-dimensional coordinates of the sample stage assumed when the final image was obtained; obtaining length information about a length per pixel of the final image at a final magnification; and finding a correlation between pixel coordinates of the final image and two-dimensional coordinates of the sample stage defining a position of the sample stage on the basis of the correlation information and of the length information.