The present invention relates to a method of aligning comprising providing a support, applying a transparent layer, patterning at least the transparent layer to produce a pattern and an alignment feature capable of scattering light, illuminating the support and the transparent layer with oblique lighting, providing an analysis system capable of sensing scattered light from the alignment feature and referencing, sensing the scattered light from the alignment feature; referencing the scattered light from the alignment feature to a position on said support; and aligning a second operation to the position.