In large area micro hot embossing, the process temperature plays a critical role to both the local fidelity of microstructure formation and global uniformity. The significance of low temperature hot embossing is to improve global flatness of embossed devices. This paper reports on experimental studies of polymer deformation and relaxation in micro embossing when the process temperatures are below or near its glass transition temperature (Tg). In this investigation, an indentation system and a micro embosser were used to investigate the relationship of microstructure formation versus process temperature and load pressure. The depth of indentation was controlled and the load force at a certain indentation depth was measured. Experiments were carried out using 1 mm thick PMMA films with the process temperature ranging from Tg-55 degrees C to Tg +20 degrees C. The embossed structures included a single micro cavity and groups of micro cavity arrays. It was found that at temperature of Tg-55 degrees C, elastic deformation dominated the formation of microstructures and significant relaxation happened after embossing. From Tg-20 degrees C to Tg, plastic deformation dominated polymer deformation, and permanent cavities could be formed on PMMA substrates without obvious relaxation. However, the formation of protrusive structures as micro pillars was not complete since there was little polymer flow. With an increase in process temperature, microstructure could be formed under lower loading pressure. Considering the fidelity of a single microstructure and global flatness of embossed substrates, micro hot embossing at a low process temperature, but with good fidelity, should be preferred.