Hot embossing is to fabricate desired pattern on the polymer substrate by pressing the patterned mold against the substrate which is heated above the glass transition temperature, and it is a high throughput fabrication method for bio chip, optical microstructure, etc. due to the simultaneous large area patterning. However, the bad pattern fidelity in large area patterning is one of the obstacles to applying the hot embossing technology for mass production. In the present study, PDMS pad was used as a cushion on the backside of the micro-patterned 4 inch Si mold to improve the pattern fidelity over the 4 inch PMMA sheet by increasing the conformal contact between the Si mold and the PMMA sheet. The pattern replicability improvement over 4 inch wafer scale was evaluated by comparing the replicated pattern height and depth for PDMS-cushioned Si mold against the rigid Si mold without PDMS cushion.