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We provide a new method for the selective surface patterning of microfluidic chips with hydrophobic fluoropolymers which is demonstrated by the fabrication of hydrophobic valves. It enables efficient optical quality control for the surface patterning thus permitting the low-cost production of highly reproducible hydrophobic valves. Specifically, a fluoropolymer-solvent-dye solution based on carbon black (CB) is presented which creates superhydrophobic surfaces (contact angle = 157.9deg) on chips made from cyclic olefin copolymer (COC). It further provides good visibility for the quality control (QC) in polymer labs-on-a-chip and increases the burst pressure of hydrophobic valves. Finally, an application which aims for the amplification of mRNA on-chip and relies on the defined flow control by hydrophobic valves is presented. Here, the QC in combination with the Teflon-CB coating improves the average standard deviation of the burst pressures from 14.5% down to 6.1% compared to solely Teflon-coated valves.