Hot embossing process has been considered as one of the most cost-efficient and fast processes in the manufacturing of micro or nano components. This paper is focus on the numerical simulation and experimental investigation of micro hot embossing process with amorphous thermoplastic polymers. The thermal and dynamical mechanical analysis have been effectuated in order to identify the polymers’ physical behaviour during hot embossing process. Generalized Maxwell model has been proposed to describe the polymer viscoelastic behaviour in the numerical simulation. The micro-fluidic devices with the cavity dimension eq. to about 200 µm in PMMA plate (thickness eq. to 2 mm) have been elaborated by the hot embossing process. The developed hot embossing experimental system shows low cost and short production cycle of the elaboration of micro-fluidic devices based on amorphous thermoplastic polymers. The comparison between the numerical simulation and experiment elaboration shows proper agreement for the prediction of the polymer substrate deformation in the replication of micro-fluidic device with hot embossing process.