A includes arranging a substrate in a working region of a first particle beam column and a second particle beam column; producing a desired target structure on the substrate by directing a first particle beam generated by the first particle beam column at a multiplicity of sites of the substrate to deposit material thereon or to remove material therefrom; repeatedly interrupting the production of the desired target structure and producing a marking on the substrate by directing the first particle beam onto the substrate and continuing the production of the desired target structure; and capturing positions of the markings on the substrate by directing a second particle beam produced by the second particle beam column onto the markings on the substrate, and detecting particles or radiation which are produced in the process by the second particle beam on the substrate.