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An axial flow cyclone for removing nanoparticles was tested for collection efficiency. Data were validated numerically in vacuum conditions of several Torrs, with flow rates of 0.35-0.57 slpm. The experimental cutoff aerodynamic diameter of the cyclone ranged from 21.7 to 49.8 nm. A 3-D numerical simulation was conducted first to calculate detailed flow and pressure fields, then a Brownian Dynamics simulation was done to determine the collection efficiency of nanoparticles. Both centrifugal force and Brownian diffusion were taken into account. The simulated results for both pressure drop and cutoff aerodynamic diameter are in good agreement with the experimental data. In comparison, previous theories using simplified tangential flow field assumption are not able to predict collection efficiencies accurately. The numerical model developed in this study can facilitate cyclone design to classify valuable nanopowders below a certain diameter, or to remove toxic nanoparticles from the vacuum exhaust of process chambers commonly used in high-tech industries.