A combined soft lithographic transfer‐printing and patterning method of highly fluorinated polymers was investigated aiming to establish a facile surface treatment protocol for various substrates. Spin‐coated layers of poly(1H,1H,2H,2H‐perfluorodecyl methacrylate) (PFDMA) on patterned polydimethylsiloxane (PDMS) molds were transfer‐printed successfully on silicon, glass, aluminum substrates, resulting in the well‐controlled production of nano to micrometer‐scale periodic structures. With careful optimization of the dimension and density of the PFDMA patterns, it was possible to achieve a water contact angle as high as 175° on the transfer‐printed highly fluorinated polymer film. One of the advantages of the transfer‐patterning method is that highly fluorinated polymer films can be printed on curved surfaces while retaining their superhydrophobic and corrosion‐prevention character. In addition, the transfer‐printed PFDMA layers on the glass plates showed enhanced light transmission, which led to the extraction of 10% more light when they were applied to the emitting side of green organic light‐emitting devices. The micro‐patterned PFDMA surfaces also exhibited a significantly reduced level of bacterial adhesion when they were incubated in human bile juice. These results strongly suggest that the proposed facile transfer‐patterning protocol of highly fluorinated polymer films can be a suitable surface‐treatment technique for implantable electronic devices that exhibit improved device performance and anti‐biofouling nature. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45184.