Propagation of Rayleigh traveling waves from a gas on a nanotube surface activates a macroscopic flow of the gas (or gases) that depends critically on the atomic mass of the gas. Our molecular dynamics simulations show that the surface waves are capable of actuating significant macroscopic flows of atomic and molecular hydrogen, helium, and a mixture of both gases both inside and outside carbon nanotubes (CNT). In addition, our simulations predict a new “nanoseparation” effect when a nanotube is filled with a mixture of two gases with different masses or placed inside a volume filled with a mixture of several gases with different masses. The mass selectivity of the nanopumping can be used to develop a highly selective filter for various gases. Gas flow rates, pumping, and separation efficiencies were calculated at various wave frequencies and phase velocities of the surface waves. The nanopumping effect was analyzed for its applicability to actuate nanofluids into fuel cells through carbon nanotubes.