Organosilicon coatings provide good optical and mechanical properties and are excellent candidates for the modification of the surface energy of polymers. These coatings can be deposited by plasma polymerization of hexamethyldisiloxane (HMDSO) under atmospheric pressure and at room temperature. The resulting films can range from soft, hydrophobic layers (SiO xC yH z) to hard, hydrophilic layers (SiO x), depending on the plasma composition.We have developed a process for the deposition of coatings of 50-500. nm thickness on polymer PS and COC substrates. The surface energy could be varied between 20 and 75. mN/m which correspond to water contact angles between 110° and 5°.A new dielectric barrier discharge (DBD) plasma mini reactor was designed which allows in-line patterned deposition of SiO x and SiO xC yH z. Small channels, incorporated in the polymer product or electrode of the reactor, allowed local deposition of the films, using only small amounts of helium and HMDSO. As a test case, the channels of a lab-on-a-chip device were given locally hydrophilic and hydrophobic coatings after bonding of lid and substrate. © 2011 Elsevier B.V.