Polyethylene oxide stabilized nanoparticles are becoming increasingly important as a means of delivering and targeting therapeutics. Processing and purifying these nanomedicines has become increasingly important. Ultrafiltration studies were performed on sterically-stabilized nanoparticle systems formed by Flash NanoPrecipitation and charge-stabilized latexes formed by emulsion polymerization for the purposes of concentration-diafiltration process optimization and characterization of membrane fouling. The nanoparticle systems were compared against similar studies done on bovine serum albumin to elucidate the mechanisms of stabilization and membrane fouling based on hydrodynamic models. As the only scalable method for the precise concentration and purification of nanoparticle systems, these studies provide guidance on achieving the desired specifications for different nanoparticle sizes, geometries and surface chemistries as opposed to typical protein ultrafiltration that is routinely employed in the biotechnology industry.