Mass transport mechanisms of drug release inside a pellet formulation through polymer membrane were investigated with focused ion beam scanning electron microscopy (FIB-SEM). Through careful control of imaging conditions, sub-surface cross sectional images were acquired on two controlled release membrane samples. Image analysis of porosity, pore size distribution, and pore connectivity in 3D provided a matrix of parameters to quantitatively compare samples from different formulations and processing conditions. Image-based computational fluid dynamics simulations were employed to correlate membrane microporosity with flow permeability. Through high resolution FIB-SEM characterization, quantitative microporosity analysis, and mechanistic investigations of flow via image-based simulations, it was found that a 10% difference in the water content of the mixed aqueous-organic solvent used to dissolve polymers had a significant impact on the controlled release performance. This approach provides an analytical avenue to evaluate effects of permeation enhancers, solvents, and other process conditions on controlled release formulations.