A new class of printing strategies is described for the manufacture of microstructures and nanostructures. This class collectively is referred to as molecular transfer lithography (MxL). The approach is based on the room-temperature fabrication of water-soluble polymer templates by spin casting a polyvinyl alcohol film-forming solution to replicate surface patterns. The templates are useful not only for pattern formation, but also for materials transfer printing, employing a low-cost, convenient, biocompatible chemical approach to high-resolution processing. Results are provided to demonstrate deep submicrometer feature sizes of holes, pillars and lines, 3-D patterns, materials transfer printing of metallic thin films, planarization of wafer topography, and water-soluble polymer templates for 100- and 200-mm wafer patterning. The alignment tooling is discussed and it is shown that MxL can be adapted for use on standard contact aligners with a replacement of the quartz photomask with a water-soluble polymer template to improve resolution without a change of equipment. A high-throughput alignment system for MxL is also discussed. The MxL class of pattern formation and materials transfer printing strategies is differentiated with respect to imprint lithography and soft lithography methods. © 2004 Society of Photo-Optical Instrumentation Engineers.