A lithography system for generating grating structures is provided having a multiple column imaging system located on a bridge capable of moving in a cross-scan direction, a mask having a grating pattern with a fixed spatial frequency located in an object plane of the imaging system, a multiple line alignment mark aligned to the grating pattern and having a fixed spatial frequency, a platen configured to hold and scan a substrate, a scanning system configured to move the platen over a distance greater than a desired length of the grating pattern on the substrate, a longitudinal encoder scale attached to the platen and oriented in a scan direction and at least two encoder scales attached to the platen and arrayed in the cross-scan direction wherein the scales contain periodically spaced alignment marks having a fixed spatial frequency.