A target structure such as an alignment mark on a semiconductor substrate becomes obscured by an opaque layer so that it cannot be located by an alignment sensor. A position for the mark is determined using an edge position sensor and relative position information that defines the position of the mark relative to one or more edge portions of the substrate is stored prior to formation of the opaque layer. A window can be opened in the opaque layer, based on the determined position. After revealing the target structure, the alignment sensor can, if desired, measure more accurately the position of the target structure, for use in controlling a further lithographic step. The edge position sensor may be a camera having an angle-selective behavior. The edge position sensor may be integrated within the alignment sensor hardware.