We investigated the plasma etching of polysiloxane intended for use in cochlear implants as a protection layer. The processing was performed using fluorine-based chemistry ionized in RIE (Reactive Ion Etching) or ICP (Inductively Coupled Plasma) discharge. The effect of temperature on polysiloxane etch rate and the resulting surface morphology was examined. XPS was employed to determine chemical changes induced by plasma treatment. The cytotoxicity on a cell line was observed in order to estimate suitability of plasma processed silicone elastomer for use in biomedical applications. This paper presents the selected results, which reveals how the polysiloxane surface properties can change depending upon plasma treatment conditions. Exemplary micro devices encapsulated in plasma treated silicone elastomer are also shown.