In this paper we develop a model describing the ballistic transport of chemical precursor species for an atomic layer deposition (ALD) process. In the application we consider, pore geometry or surface properties of nanoporous materials are modified using ALD, taking advantage of its potential for conformal deposition in high-aspect-ratio structures. Because of the very large Knudsen number corresponding to these processes, the transport of gas-phase species inside the nanostructures takes place in a purely ballistic manner. Precursor transmission probability functions describing the fluxes between the pore surface features are developed and compared to previously published results. The transport model elements are then coupled to ALD surface-reaction models, spatially discretized, and integrated over each precursor exposure period to determine the pore spatial surface reaction extent profile. Predictions from our dynamic model are then compared to four previously published studies of ALD in nanopores to validate our simulator, and to gain further insight into the physical mechanisms at work in ALD processes. The utility of physically based models of the type we develop can be exploited to determine optimal precursor exposure levels for ALD-based nanomanufacturing operations.