Recently nano imprint lithography to fabricate photonic crystal on polymer is preferred because of its simplicity and short process time and ease of precise manufacturing. But, the technique requires the precise mold as an imprinting tool for good replication. These molds are made of the silicon, nickel and quartz. But this is not desirable due to complex fabrication process, high cost. So, we describe a simple, precise and low cost method of fabricating PDMS stamp to make the photonic crystals. In order to fabricate the PDMS mold, we make the original pattern with designed hole array by finding the optimal electron beam writing condition. And then, we have tried to fabricate PDMS mold by the replica molding with ultrasonic vibration and pressure system. We have used the cleaning process to solve the detaching problem on the interface. Using these methods, we acquired the PDMS mold for photonic crystals with characteristics of a good replication. And the accuracy of replication shows below 1% in 440nm at diameter and in 610nm at lattice constant by dimensional analysis by SEM and AFM.