Nanoimprint lithography is a fast replication technology for structures with sizes ranging from micrometer down to few nanometer range. This article describes the technology for imprinting of polymer substrates as well as spin-on polymers by using soft working stamp materials on a fully automated hot embossing system, the EVG (R) 750, built to use this rapid replication processes. By utilizing soft working stamps, the authors demonstrate the possibility to replicate, in fully automated mode, both high-aspect ratio features in thermoplastic materials as needed for microfluidic lab-on-chip applications as well as high resolution features down to 50 nm in polymer that can be used as templates for pattern transfer in the fabrication of plasmonic substrates for biosensing applications.