A N95 face-piece respirator and a 3M air filter composed of non-woven polypropylene filter material were investigated for their multi-scale microstructure and resulting filtration performance. Filtration mechanisms of each system are found and quantified. Both media showed a gradually decrease of the most penetrating particle size with respect to an increase in face velocity or surface charge density. Increasing the face velocity and porosity dramatically degraded the collection efficiency in the 3M filter rather than in the N95 system. We exploited three-dimensional X-ray tomography to characterize the morphological and geometrical properties of the fiber arrangement and deposition of aerosol on the fiber surface. Tuning the most predominant material parameters to achieve a precedence in lower pressure drop or higher collection efficiency in a specifically captured particle size range is of great requisite to a peculiar application of the filter media.