Soft UV-imprint lithography at sub-micron dimensions was achieved in thin films of photopolymer resist. The imprinting was enabled by overcoming resist absorption by polydimethylsiloxane (PDMS) through surface treatment with a layer of (heptadecafluoro-1,1,2,2-tetrahydrodecyl)dimethylchlorosilane. Characterization of the composite molds was done by X-ray photoelectron spectroscopy, nanoindentation, and contact angle measurements. PDMS molds treated with fluoroalkylsilane layer were used to imprint into thin films (70–630 nm) of UV curable resins consisting of either polyurethanes or acrylates, replicating with high fidelity features over the surface of wafer substrates. The use of these highly conformal PDMS molds allowed the patterning of functional materials including gold and aluminium by a simple imprint lithographic technique. This is the first report of the use of modified PDMS surfaces in an imprint process that enables the transfer of sub-micron patterns to underlying layers for device structure fabrication. The patterned features were studied with atomic force microscopy, scanning electron microscopy, and optical microscopy.