Using an imaging system in relation to a plurality of material layers is described, the material layers being separated by a distance greater than a depth of field of the imaging system. A focal plane of the imaging system and a first of the plurality of material layers are brought into correspondence. A first image including at least a portion of the first material layer having a first feature of interest thereon is stored. The focal plane of the imaging system and a second of the plurality of material layers are brought into correspondence. A second image including at least a portion of the second material layer having a second feature of interest thereon is acquired. The first and second images are processed for automatic computation of an alignment measurement between the first and second features of interest.