A method of patterning a substrate comprising first and second fields with a template, the template having a mold and a plurality of alignment forming areas and a plurality of template alignment marks, the method comprising: positioning a material on the first field of the substrate and a plurality of regions of the substrate, the plurality of regions laying outside of the first and second fields; positioning the mold and the substrate such that a desired spatial relationship between the mold and the first field of the substrate is obtained to define a pattern in the material on the first field of the substrate while concurrently defining a plurality of substrate alignment marks with the material in the plurality of regions of the substrate in superimposition with the plurality of alignment forming areas of the template; positioning a material on the second field of the substrate; and positioning the mold and the substrate to obtain a desired spatial relationship between the plurality of template alignment marks and the plurality of substrate alignment marks such that a desired spatial relationship between the mold and the second field of the substrate is obtained to define a pattern in the material on the second field of the substrate.