The characterization of encapsulation efficiency and in vitro drug release from nanoparticle-based formulations often requires the separation of nanoparticles from unencapsulated drug. Inefficient separation of nanoparticles from the medium in which they are dispersed can lead to inaccurate estimates of encapsulation efficiency and drug release. This study establishes dynamic light scattering as a simple method for substantiation of the effectiveness of the separation process. Colistin-loaded liposomes, as an exemplar nano-sized delivery particle, were diluted to construct a calibration curve relating the amount of light scattering to liposome concentration. Dynamic light scattering revealed that, in the case of ultracentrifugation and centrifugal ultrafiltration, approximately 2.9% of the total liposomes remained in supernatants or filtrates, respectively. In comparison, filtrates obtained using pressure ultrafiltration contained less than 0.002% of the total liposomes from the formulation. Subsequent release studies using dialysis misleadingly implied a slow release of colistin over >48 h. In contrast, pressure ultrafiltration revealed immediate equilibration to the equilibrium distribution of colistin between the liposome and aqueous phases upon dilution. Pressure ultrafiltration is therefore recommended as the optimal method of choice for studying release kinetics of drug from nanomedicine carriers.