The invention relates to a method for processing a substrate with a focussed particle beam which incidents on the substrate, the method comprising the steps of: (a) generating at least one reference mark on the substrate using the focused particle beam and at least one processing gas, (b) determining a reference position of the at least one reference mark, (c) processing the substrate using the reference position of the reference mark, and (d) removing the at least one reference mark from the substrate.