Abstract In large areas of micro hot embossing, process temperature plays a critical role to both the local-area fidelity and global uniformity of microstructure formation. Higher embossing temperature could improve structure fidelity, however, at the expense of demoulding easiness. Micro embossing at the lowest possible temperature with acceptable fidelity can improve global flatness after demoulding. This study focuses on polymer deformation and recovery in micro embossing when the process temperature is below the polymer glass transition temperature (Tg). PMMA (Polymethyl Methacrylate) substrates (Tg = 105°C) were employed with the process temperature ranging from 25°C to its Tg. At temperature below Tg −55°C, significant recovery occurred after processing, but permanent structures could still be formed with sufficiently high applied stress. With an increase in temperature, plastic deformation increased and was the dominant polymer deformation mode for permanent cavities formation. However, the formation of protrusive structures was not complete since there was little polymer flow. The polymer will lose its storage modulus at an even higher temperature and microstructures could be formed with high fidelity. A compromise between local fidelity of embossed patterns and global flatness of substrate has to be reached in micro hot embossing. [ABSTRACT FROM AUTHOR]