Alignment marks for use on substrates. An exemplary implementation provides phase depth control. A grating mark, for example, can be etched on a silicon wafer with sub-wavelength segmentation in the spacing portion of the alignment grating's period. The sub-wavelength segmentation can be applied to the spaces or to the lines, or both, of an alignment grating to control the phase depth of the grating. By applying segmentation with a period smaller than the alignment light wavelength in either the space(s) and/or in the line(s) of the grating, the effective refractive index in that region can be manipulated. This change in the effective index will result in a change in the phase depth (optical path length). By varying the duty cycle of the sub-wavelength segmented region, the effective refractive index can be controlled, thereby providing selective control over the phase depth.