The present paper studies the separation phenomenon for argon–helium mixture outflowing through a convergent–divergent micronozzle into a vacuum. We numerically investigate the effect of the geometrical parameters of the micronozzle and gas rarefaction (Knudsen number is varied in range ≈0.01−100). Simulations were performed using the event-driven molecular dynamics method. Performed analysis revealed several interesting and important features of the separation process. First, it was shown that separation in the present problem results mainly from a lateral component, which appears when significant curvature of gas streamlines is present. Second, it was demonstrated how the fine-tuning of micronozzle geometry can enhance separation efficiency. At the same time, the simplest microslit arrangement (a microchannel without converging and diverging parts) was shown to provide results comparable to micronozzles and may be preferable due to its manufacturing simplicity. Then, it was shown that the position of the product gas selector is crucial for effective separation and its proper placement brings more influence than the geometry of the micronozzle itself. Finally, it was shown that maximal purity of product gas can be obtained in a peripheral area in transitional and slip flow regimes inside the micronozzle. Therefore, for effective separation, there is no need to achieve high rarefaction levels inside the micronozzle.