The application of a three dimensional, self-aligning shadow mask in (110)-oriented silicon for thin-film metal deposition is discussed. this shadow mask is used for the deposition of metal tracks on the bottom of structures with vertical sidewalls, i.e., the patterning of metal catalytic patches underneath the membrane that covers the deep flow channel of a high-temperature gas microreactor. The accuracy of this patch definition-pattern spreading-is investigated for rhodium and platinum as a function of the mask-to-substrate distance. The pattern of sputter-deposited patches is subject to pattern spreading when the gap between the shadow mask and the substrate is nonzero. The experimental patch widening shows a square root dependency on the gap size. Via numerical simulations of molecular gas flows using a direct simulation Monte Carlo method, it is shown that there is excellent agreement between the observed experimental data and this model taking into account values for the sticking (gamma) and accommodation (a) coefficients of the atoms on the walls of the shadow mask below unity (i.e., gamma\=0.5 and alpha=0.1), and a baseline shift due to curvature and/or bending of the shadow mask and/or substrate. (c) 2007 American Vacuum Society.