The Hot Embossing Lithography(HEL) as a method fur the fabrication of the nanostructure with polymer is becoming increasingly important because of its simple process, low cost, high replication fidelity and relatively high throughput. In this paper, we carried out experimental studies and numerical simulations in order to understand the viscous flow of the polymer (PMMA) film during the hot embossing process. To grasp the characteristics of the micro patterning rheology by process parameters (embossing temperature, pressure and time), we have carried out various experiments by using the nickel-coated master fabricated by the deep RIE process and the plasma sputtering. During the hot embossing process, we have observed the characteristics of the viscoelastic behavior of polymer. Also, the viscous flow during the hot embossing process has been simulated by the continuum based FDM(Finite Difference Method) analysis considering the micro effect, such as a surface tension and a contact angle.