An UV/thermal hybrid nanoimprint lithography system was designed and implemented for the pattern transfer to flexible substrates. This system can utilize a plate stamp, roll stamp, and film stamp. For all cases of using those stamps, this system is also switchable an UV or thermal nanoimprint lithography mode. This paper shows how to design the heating and UV curing plates and proposes how to change them easily. Because the pressure condition and the speed of the press roller varies by the characteristics of the stamp and substrate, all the parameters related to the nanoimprint lithography have to adjustable. Some transferred patterns are shown in this paper to verify the performance of the hybrid nanoimprint lithography system. The flexible substrates with nano-scale patterns on them will be key components for next generation technologies such as flexible displays, bendable semi-conductors, and solar cells.