The performance characteristics of virus filtration membranes are strongly influenced by the underlying pore size and morphology of the membrane, but the available characterization techniques provide only limited information on these properties. A new methodology was developed for probing the internal pore size and structure of different virus filtration membranes by direct visualization of captured gold nanoparticles using scanning electron microscopy (SEM). SEM images were obtained using both hollow fiber (Planova (TM) 20 N and BioEX) and flat sheet (Viresolve (R) Pro and Ultipor (R) DV20) membranes after challenging with 20, 40, and / or 100 nm gold nanoparticles. The images were used to identify the location of individual nanoparticles and to calculate the nanoparticle distribution through the depth of the filter (using ImageJ software). The results clearly demonstrate the very different pore structures within these filters and their impact on nanoparticle capture, providing important insights into the performance characteristics of these virus filtration membranes.