A method of determining an offset between an imprint template and a substrate using an alignment grating on the imprint template and an alignment grating on the substrate is disclosed. The method includes bringing the imprint template alignment grating and the substrate alignment grating sufficiently close together such that they form a composite grating, directing an alignment radiation beam at the composite grating while modulating the relative position of the imprint template and the substrate, detecting the intensity of alignment radiation which is reflected from the composite grating, and determining the offset by analyzing modulation of the detected intensity.