Recent advances in the development and application of self-assembly templating techniques have opened up the possibility of tailoring membranes for specific separation problems. A new self-assembly processing route to generate inorganic membrane films has made it feasible to finely control both the three-dimensional (3D) porosity and the chemical nature of the adsorbing structures. Chemical sites can be added to a porous membrane either after the inorganic scaffolding has been put in place or, alternatively, chemical sites can be co-assembled in a one-step process. To provide guidance to the optimized use of these ‘designer’ membranes we have developed a substantial modeling program that focuses on permeation through porous materials. The key issues that need to be modeled concern 1) the equilibrium adsorption behavior in a variety of 3D porous structures, ranging from straight pore channels to fractal structures, 2) the transport (i.e. diffusion) behavior in these structures. Enriching the problem is the presence of reactive groups that may be present on the surface. An important part of the design of actual membranes is to optimize these reactive sites with respect to their strength as characterized by the equilibrium constant, and the positioning of these sites on the adsorbing surface. What makes the technological problem challenging is that the industrial application requires both high flux and high selectivity. What makes the modeling challenging is the smallness of the length scale (molecular) that characterizes the surface reaction and the confinement in the pores. This precludes the use of traditional continuum engineering methods. However, we must also capture the 3D connectivity of the porous structure which is characterized by a larger than molecular length scale. We will discuss how we have used lattice models and both Monte Carlo and 3D density functional theory methods to tackle these modeling challenges.