A method of aligning a template and a substrate for imprint lithography involves using a mask pattern of the template and a luminescent marker pattern of the substrate, the method including aligning the template mask pattern and the substrate marker pattern using a radiation intensity measurement of radiation emitted by the luminescent marker pattern and having passed the template mask pattern. The mask pattern and the luminescent marker pattern may each be shaped to provide a turning point in the intensity of detected radiation emitted from the marker pattern, and passing through the mask pattern to a detector, as a function of relative displacement at the aligned position. The displacement of the template and substrate may be aligned by identifying the turning point in radiation intensity. The marker pattern may be fluorescent with the emitted radiation excited by a radiation source.