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Differential pumping maintains different gas pressures in connected regions by restricting the connecting gas flow and pumping each region separately. A small aperture or narrow tube limits the vacuum conductance between stages.

In the molecular flow regime, a connection with conductance $C$ carries throughput $Q=C(p_1-p_2)$. A downstream stage pumped at effective speed $S$ has $S{p}_2=C(p_1-p_2)$ in steady state, giving $p_2/p_1=C/(S+C)$. This lets a source operate at a higher pressure while an adjacent particle beam travels in a better vacuum.^[ref]

A molecular beam skimmer is a small aperture, commonly at the tip of a cone, that transmits the central part of an expanding molecular beam into a downstream chamber. It separates source and measurement regions so that differential pumping can maintain a lower background pressure after the source. Its geometry selects directions; that selection alone does not give all transmitted molecules the same speed.

The surface also perturbs the beam. At high source number density, particles reflected from the skimmer walls can collide with the incoming flow and create shock waves, reducing and heating the transmitted beam. A 2017 experiment cooled the skimmer and measured a beam-flux increase of about eightfold under its tested conditions. A pulsed plasma glow made the disturbed flow visible; cooling reduced reflected momentum and, at lower temperatures, promoted adsorption. This tests why a narrower geometric opening is not a complete model of a real skimmer.^[ref]