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We describe our reliable methodology for fabricating a complex programmable microvalve array (PMA) and its integration with a glass microcapillary electrophoresis chip. This methodology is applicable to any device that requires multilayered PDMS, multiple alignment processes, selective PDMS bonding, and multilayered integration with downstream sensing systems. Along with the detailed step-by-step process, we discuss essential quality assurance checks that can be performed throughout fabrication to assist in troubleshooting and maximizing chip yield. • Comprehensive instructions for designing and fabricating a programmable microvalve array. • Selective bonding of PDMS and glass by microcontact printing. • Numerous quality control procedures to boost chip yield.