A contact lithography alignment system (500) and methods (100, 200, 400) use nanoscale displacement sensing and estimation (nDSE) 300, 300' to maintain an alignment and compensate for a disturbance of one or more objects (510) during contact lithography. A method (100) of maintaining an alignment includes establishing (110) an initial alignment of one or more objects and employing (120, 200) nDSE-based feedback control of relative positions of one or more of the objects to maintain the alignment during contact lithography. A method (400) of disturbance compensation includes acquiring (410) a first image, acquiring (210, 420) a second image, estimating (220, 430) an alignment error using (120, 200) nDSE applied to the first and second images, and adjusting (230, 440) a relative position to reduce the alignment error. The contact lithography system (500) includes an optical sensor (520), a feedback processor (530, 600) providing nDSE and a position controller (540) that adjusts relative positions of one or more objects to reduce an alignment error determined using the nDSE.
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