Poly(dimethylsiloxane), PDMS, a versatile elastomer, is the polymer of choice for microfluidic systems. It is inexpensive, relatively easy to pattern, and permeable to oxygen. Unmodified PDMS is highly hydrophobic. It is typically exposed to an oxygen plasma to reduce this hydrophobicity. Unfortunately, the PDMS surface soon returns to its original hydrophobic state. We present two alternative plasma treatments that yield long-term modification of the wetting properties of a PDMS surface. An oxygen plasma pretreatment followed by exposure to a SiCl4 plasma and an oxygen-CCl4 mixture plasma both cause a permanent reduction in the hydrophobicity of the PDMS surface. We investigate the properties of the plasma-treated surfaces with X-ray photoelectron spectroscopy (XPS) and contact angle measurements. We propose that the plasma treated PDMS surface is a dynamic mosaic of high- and low-contact-angle functionalities. The SiCl4 and CCl4 plasmas attach polar groups that block coverage of the surface by low-molecular-weight groups that exist in PDMS. We describe an application that benefits from these new plasma treatments, the use of a PDMS stencil to form dense arrays of DNA on a surface.