Multilevel three-dimensional nanostructures are essential in many integrated nanoelectronic and nanophotonic applications. With the continued shrinking of critical device dimensions, extremely precise nanoscale overlay is required between multiple individual levels of these integrated devices. Multilevel nanoimprint lithography has been proposed in the literature as a potential solution to this overlay problem. In this context, self-aligned (perfectly aligned) multilevel templates (SAMT) for multilevel nanoimprint lithdgraphy are proposed in this article. By combining nanolithography, atomic layer deposition, and highly selective reactive ion etch, SAMTs can enable the fabrication of sophisticated integrated devices. Four specific self-aligned multilevel fabrication techniques have been demonstrated that result in symmetric multilevel structures, bilaterally symmetric multilevel structures, tubular structures, and asymmetric multilevel structures, all in the sub-100 nm scale. When used in conjunction with a nanoimprint lithography process, the SAMTs can enable high-throughput patterning of various nanoelectronic and nanophotonic devices using a single patterning step with perfect alignment and overlay. SAMTs further enable large area patterning, such as wafer-scale patterning and roll-to-roll patterning on flexible substrates, without compromising perfect overlay. (C) 2016 Elsevier B.V. All rights reserved.