Nanoimprint Lithography (NIL) is a high throughput replication technology for structures ranging from micrometer down to few nanometers. NIL can be divided into UV-Nanoimprint (UV-NIL) and Hot embossing (HE). The main difference between these two techniques are the material types of both template and resist, i.e transparent templates and photosensitive resists for UV-NIL and non transparent templates and thermoplastic resists for HE. Hot embossing is a low-cost, high throughput fabrication technique of disposable, polymer based devices needed for emerging point-of care diagnostic or bio-sensing applications. This paper 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 ® 750, built to use this rapid replication processes. Soft working stamps demonstrate the possibility to replicate both, high-aspect ratio features in thermoplastic materials as needed for microfluidic lab-onchip applications as well as high resolution features down to 50 nm in polymers that can be used as templates for pattern transfer in the fabrication of plasmonic substrates for biosensing applications.