Alignment system for various materials and material flows

A method and system for alignment of a tool to a workpiece in a continuous or discontinuous material flow are disclosed. The workpiece may be a portion of a web of material. An imaging system captures first and second images of the workpiece at first and second occasions respectively. Microscopic native features of the workpiece are selected, detected, tracked and/or compared in the first and second images. Based on the correspondence between, tracking or relative displacement of features as captured in the first and second images, an alignment to the workpiece is controlled. In embodiments, the workpiece and a tool, a projected image or a pattern to be imparted to the workpiece by a lithography or photolithography apparatus are aligned based upon positioning information determined from an analysis of correlated features or texture in the images. Positioning information may include a positioning error or a distortion indication.