Interstellar neutral (ISN) helium atoms penetrating the heliosphere are used to find the flow velocity and temperature of the very local interstellar medium near the heliosphere. Recently, it was found that, in addition to charge exchange collisions, elastic collisions contribute to the filtration of these atoms outside the heliopause. Momentum exchange between colliding particles related to their angular scattering modifies the properties of the primary and secondary ISN helium populations before the atoms enter the heliosphere. Here, we calculate the transport of ISN helium atoms using plasma and neutral flows from a global three-dimensional heliosphere model. We confirm earlier results based on one-dimensional calculations that the primary population is slowed down and heated by the momentum exchange. Moreover, accounting for momentum exchange in charge exchange collisions results in a faster and warmer secondary population. The paper presents how the velocity and density of these populations vary over the entrance position to the heliosphere. We point out that Maxwell distributions cannot correctly describe these populations. Finally, we calculate the expected Interstellar Boundary Explorer (IBEX) count rates and show that the filtration processes change them significantly. Consequently, future studies of IBEX or Interstellar Mapping and Acceleration Probe (IMAP) observations of ISN atoms should account for these processes.