The use of hybrid organic-inorganic materials in gas separation is a topic of great interest. One recent example is the observed increase in separation performance of polymers upon confinement in a mesoporous medium [M. Moaddeb, W.J. Koros, Journal of Membrane Science 125 (1997) 143-163]. In this paper, we use computer simulation to probe molecular level phenomena and mechanisms in such systems. Molecular dynamics simulations were employed to study the permeation of small penetrants (helium and neon) in model polymers confined between solid surfaces. A planar graphite mesopore model was used for the solid surfaces, and the polymer was modeled as polymethylene chains. The diffusion coefficients and Henry's Law solubilities of the penetrants were calculated in a variety of membrane models with varying polymer loading between the solid surfaces. The state of the polymer was varied between rubbery and glassy by changing the temperature. Changes in the microstructure and dynamics of the polymer were observed upon confinement, similar to those seen in previous literature studies. Dramatic changes in permeability and selectivity of the polymer material were also observed. The selectivity for helium over neon changed by as much as a factor of two, while the penetrant permeability changed by as much as two orders of magnitude. The polymer loading in the pore was found to be a key variable; very small changes in loading could produce order of magnitude changes in permeability. The implications of our results on the rational design of hybrid inorganic-organic separation media are discussed.