Soft lithography fabrication methods have been used enormously by MEMS researchers in recent years, due to their low cost and simplicity and batch fabrication feasibility. In this paper, a low cost and useful technique to fabricate Microstructures on a polymeric substrate by hot embossing is presented. The used master has been fabricated from SU-8 polymer on a glass substrate. The main parameters of hot embossing quality such as temperature and pressure are discussed and the optimum values are determined. The hydrophobic surface of PMMA substrate is modified to hydrophilic in order to be used in Microfluidic devises. As a good approach, Micro channels by minimum feature size of 15?m and depth of 50?m are implemented in this paper. Major advantages of this method are simplicity and low cost, because of not-complicated equipment and inexpensive materials for substrate.