A method of aligning a substrate and an imprint template is disclosed. The method includes directing an alignment radiation beam towards an imprint template alignment mark and an adjacent substrate alignment mark, the imprint template alignment mark and the substrate alignment mark each including a grating which extends in a first direction and a grating which extends in a second direction, providing relative movement between the imprint template and the substrate in the first direction and in the second direction, using an intensity detector to detect the intensity of alignment radiation redirected in the zero-order direction by the imprint template alignment mark and the substrate alignment mark during the relative movement in the first direction and in the second direction, and determining an aligned position of the imprint template alignment mark and the substrate alignment mark based upon the detected intensity.