Methods for fabricating and replicating self-aligned multi-tier nanoscale structures for a variety of cross-sectional geometries. These methods can utilize a single lithography step whereby the need for alignment and overlay in the process is completely eliminated thereby enabling near-zero overlay error. Furthermore, techniques are developed to use these methods to fabricate self-aligned nanoscale multi-level/multi-height patterns with various shapes for master templates, replica templates and nanoimprint based pattern replication. Furthermore, the templates can be used to pattern multiple levels in a sacrificial polymer resist and achieve pattern transfer of the levels into a variety of substrates to form completed large area nanoelectronic and nanophotonic devices using only one patterning step.