This paper describes F-based dry etching and resulting surface properties of biocompatible silicone elastomer. The etch rate of polysiloxane and surface morphology was found to be highly temperature dependent. An increase in temperature results in a significantly higher etch rate and a lower surface roughness. Possible mechanisms of the etching process and the roughness formation on an elastomer surface are discussed. The polysiloxane surface was proved to have hydrophobic characteristics both prior to and after plasma exposure. The results of the preliminary cytotoxicity study are very promising: cell viability on a raw and plasma treated polysiloxane was found to be very high and comparable to control. Due to the acceptable etch rate and absence of toxic contaminations, a F-containing plasma is considered an excellent method for microprocessing of silicone elastomers intended for biomedical applications.