In the free molecular flow regime the Knudsen number is significantly greater than unity. The mean free path is therefore much greater than the length scale of the flow, and molecules collide with surfaces bounding the flow more frequently than they collide with one another. In this regime there are two common approaches to modeling the flow: the direct simulation Monte Carlo (DSMC) method (which computes the trajectories of large numbers of randomized particles through the system) and the angular coefficient method. COMSOL Multiphysics uses the angular coefficient method. Completely diffuse scattering (total accommodation) and emission are assumed at all surfaces in the geometry (in practice this is often a reasonable assumption for both the reflection and emission of molecules from most surfaces and sources). The flow is computed by integrating the flux arriving at a surface from all other surfaces in its line-of-sight. Because only surfaces are considered in the calculation, the dependent variables exist only on the surfaces of the model. This method is limited to quasi-static flows, in which the fluxes change on time scales that are large compared to the average time that the molecules take to traverse the geometry. It is much faster than the DSMC method and is not subject to statistical scatter.

The Free Molecular Flow Interface () should be used to compute quasi-static molecular flows with Knudsen numbers greater than 10. The flux, pressure, and number density are solved for on all surfaces. The effect of surface temperature is also accounted for, and the heat flux due to the molecules themselves is available. It is also possible to compute the number density of gas molecules on points, lines, and even domains interior to the bounding surfaces of the flow.