Successful implementation of a high-speed roll-to-roll nanoimprinting technique for continuous manufacturing of electronic devices has been hindered due to lack of simple substrate preparation steps, as well as lack of durable and long lasting molds that can faithfully replicate nanofeatures with high fidelity over hundreds of imprinting cycles. In this work, we demonstrate large-area high-speed continuous roll-to-roll nanoimprinting of 1D and 2D micron to sub-100 nm features on flexible substrate using perfluoropolyether (PFPE) composite molds on a custom designed roll-to-roll nanoimprinter. The efficiency and reliability of the PFPE based mold for the dynamic roll-to-roll patterning process was investigated. The PFPE composite mold replicated nanofeatures with high fidelity and maintained superb mold performance in terms of dimensional integrity of the nanofeatures, nearly defect free pattern transfer and exceptional mold recovering capability throughout hundreds of imprinting cycles.