A method for forming an aligned mask comprises etching a reference mark on a substrate to demarcate a boundary of an etch region; forming an etch mask on the substrate, using an exposure setting, the etch mask having a boundary; and measuring a distance between the reference mark and the boundary. When the measured distance is outside a margin of a target distance, then the etch mask is removed from the substrate, the exposure setting is changed, a next etch mask is formed using the changed exposure setting, and said measuring is repeated. A set of reference marks can be etched on a top level in a set of levels to demarcate boundaries of etch regions. An etch-trim process can be performed to form steps in the set of levels, wherein the etch-trim process includes at least first and second etch-trim cycles using first and second reference marks.