Linear polystyrene of different weight averaged molecular weight (M w =58kg/mol and 353kg/mol) and a narrow molecular weight distribution was imprinted to point out differences in the flow behaviour caused by the polymer’s molecular weight in a typical hot embossing/thermal nanoimprint process. Residual layer thickness and uniformity as well as defects were taken as a measure to qualify the imprint process. Since polymer viscosity is addressed as the main material parameter, a full thermo-mechanical characterisation of the two polymers via parallel plate dynamic viscosimetry was performed prior to imprint. The main process parameter responsible for viscosity, the temperature, was varied from about 30 to 150K above the glass transition. In addition the amount of polymer supplied for the process was varied, i.e. the initial spin-coated polymer layer thickness. Situations representing ‘underfilling’, ‘filling’ and ‘overfilling’ of the stamp cavities in specific regions were investigated. Squeezed flow simulations were performed taking into account the increase of pattern size and the filling of cavities during the ongoing imprint, which have substantial impact on the residual layers obtained. The results show that shear thinning is an issue in a high pressure hot embossing system. It governs the initial phase of the imprint featuring a rapid decrease of the polymer height. From theoretical considerations, a model could be derived for the imprint procedure under shear thinning in a constant pressure system which was able to interpret the observed phenomena. Despite the macroscopic nature of the thermo-mechanical analysis, the standard viscosimetric data for the polymers appeared to be sufficient to understand the experimental results.