A system for the fabrication of patterned miniature structures, such integrated circuits, includes a continuous, flexible substrate that is transported by rollers to a series of processing stations. To ensure proper alignment amongst the various stations, the substrate is provided with at least one fiducial that is raised above its top surface a height that maximizes optical contrast when viewed interferometrically. At least one processing station includes an optical device that is capable of both interferometrically identifying the fiducial for alignment purposes and subsequently illuminating the substrate with a modifiable light pattern as part of a photolithographic process. Fiducials can also be used to identify gross geometric variances in the substrate caused by external factors, such as heat and moisture. In turn, a web adjustment element can be used to apply selective heat or tension to the substrate in order to correct such geometric variances.