A method for operating a particle beam microscope comprising detecting light rays or particles which emanate from a structure, wherein the structure comprises at least one of: at least a portion of a surface of an object and at least a portion of a surface of an object holder of the particle beam microscope; generating a surface model of the structure depending on the at least one of the detected light rays and the particles; determining a position and an orientation of the surface model of the structure relative to the object region; determining a measurement location relative to the surface model of the structure; and positioning the object depending on the generated surface model of the structure, depending on the determined position and orientation of the surface model of the structure, and depending on the determined measurement location.