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Abstract Sterilization of skin prior to surgery is challenged by the reservoir of bacteria that resides in hair follicles. Atmospheric pressure plasma jets (APPJs) have been proposed as a method to treat and deactivate these bacteria as atmospheric plasmas are able to penetrate into structures and crevices with dimensions similar to those found in hair follicles. In this paper, we discuss results from a computational investigation of an APPJ sustained in helium flowing into ambient air, and incident onto a layered dielectric similar to human skin in which there are idealized hair follicles. We found that, depending on the location of the follicle, the bulk ionization wave (IW) incident onto the skin, or the surface IW on the skin, are able to launch IWs into the follicle. The uniformity of treatment of the follicle depends on the location of thefirst entryof the plasma into the follicle on the top of the skin. Typically, only one side of the follicle is treated on for a given plasma pulse, with uniform treatment resulting from rastering the plasma jet across the follicle over many pulses. Plasma treatment of the follicle is sensitive to the angle of the follicle with respect to the skin, width of the follicle pocket, conductivity of the dermis and thickness of the underlying subcutaneous fat layer, the latter due to the change in capacitance of the tissue.