Fiducial markers are provided on patterned arrays of the type that may be used for molecular analysis, such as sequencing. The fiducials may have configurations that enhance their detection in image or detection data, that facilitate or improve processing, that provide encoding of useful information, and so forth. Examples of the fiducials may include features and materials that are provided on or in the support of the array and that return at least a portion of incident light by reflection. The fiducials may form gratings or other encoding configurations that assist in image processing, alignment, or other aspects of processing of the array.