This study reports the pattern definable and low cost fabrication of nanopatterned conducting polymer film on flexible substrates. Noble nanopatterned polymer hard template was fabricated by using nanoimprint lithography (NIL) and used for electropolymerization of conducting polymer. Conducting polymer was electrochemically deposited on the template and transferred over to flexible substrates. Eventually conducting polymer films with various nanopatterns were fabricated on flexible substrates. High pattern definability was achieved by nanoimprinted polymer template, which was molded from lithographically fabricated stamp. Low cost fabrication was accomplished due to low cost NIL, reusable polymer templates, and low material consumption of electrodeposition. The electrodeposited films were transferred using double sided tape. Because the templates are made of flexible polymer, the transfer bonding method applied in this study is adaptable to both wafers and flexible polymer substrates. The fabricated nanopatterned conducting polymer film can be applied to gas sensors, super capacitors, super wetting films, and neuron interfaces due to its characteristic of high surface to volume. For an illustrative application, the gas sensing properties of films were tested. The result showed enhanced sensing characteristic with nanopatterned film, which are attributed to the high surface to volume ratio of nanopatterned films.