Human studies provide valuable information on components or analytes recovered from exhaled breath, but there are limitations due to inter-individual and intra-individual variation. Future development and implementation of breath tests based on aerosol analysis require a clear understanding of how human factors interact with device geometry to influence particle transport and deposition. The computational fluid and particle dynamics (CFPD) algorithm combines (i) the Eulerian approach to fluid dynamics and (ii) the Lagrangian approach to single particle transport and deposition to predict how particles are carried in fluids and deposited on surfaces. In this work, we developed a 3D multiscale CFPD model to provide insight into human factors that could be important to control or measure during sampling. We designed the model to characterize the local transport, spatial distribution, and deposition of polydisperse particles in a single impaction filter of a commercial aerosol collection device. We highlight the use of decoupling numerical strategies to simultaneously quantify the influence of filter geometry, fluid flowrate, and particle size. Our numerical models showed the remarkable effect of flowrate on aerosol dynamics. Specifically, aerosol mass deposition, spatial distribution, and deposition mechanisms inside the filter. This work as well as future studies on the effect of filter geometry and human factors on aerosol collection will guide the development, standardization, and validation of breath sampling protocols for current and emerging breath tests for forensic and clinical applications.