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Integration of microfluidic systems within an integrated circuit is a promising approach for developing new generation of bioelectronic noses. In this paper, we present fabrication techniques for a microsystem consisting of an array of ion sensitive field-effect transistors in hydrophilic cell under a hydrophobic membrane. Sacrificial aluminum etching technique was used to form capillary microchannels, and self-assembled monolayers were used for achieving hydrophobic properties of the membrane and hydrophilic properties of the microchannels. The developed microsystem with membrane pore size 4 μm2 was shown to hold liquid, achieving stable air-liquid interface for extraction of molecules from gaseous phase.