In this chapter, we describe the fabrication and use of microfluidic capillary systems (CSs) made in soft, transparent polydimethylsiloxane (PDMS). Sixteen microfluidic CSs, each containing a loading pad, a microchannel, and a capillary pump are engraved in a single PDMS chip. The CSs are used for two applications, firstly to pattern fibronectin on glass surfaces to locally control the adhesion of cultured cells to the substrate, and secondly to carry out multiplexed miniaturized immunoassays.