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In this paper, we report on stable liquid-air interfaces and high-aspect-ratio polymer micromembranes with complex and controlled structures formed within microfluidic channels. Selective alkanethiol treatment on gold and copper surfaces is employed to create hydrophilic-hydrophobic boundaries between glass and these metal surfaces within microchannels. Robust liquid-air interfaces, featured with different 3-D structures, are formed at these boundaries. The process for creating these liquid-air interfaces is highly reproducible. Simulations are conducted to further study the liquid-air interfaces. The liquid-air interfaces are then utilized for interfacial polymerization. Two immiscible liquid phases containing the reagents react and generate polymer micromembranes within microfluidic channels. Formed following the hydrophilic-hydrophobic boundaries, these membranes have not only complex footprints on the substrates but also different configurations in the -direction. Here, we demonstrate high-quality and complex 3-D nylon micromembranes fabricated in microchannels using this method.