Stencil masks are key to charged particle projection lithography, in particular for ion projection lithography. To fulfill pattern printing requirements in the sub-70 nm regime, excellent thickness uniformity and thermal emissivity control are critical parameters for high quality stencil mask fabrication. We propose and demonstrate a technique based on infrared variable angle spectroscopic ellipsometry (IR-VASE) to measure these parameters with adequate accuracy and precision. The refractive index of the Si membrane was evaluated using a Sellmeier dispersion model combined with a Drude model. Because of its spectral range from 2 to 33 mum, the IR-VASE method is sensitive to the thickness of layers as well as to the concentration and profile of Si membrane doping.