An approximate representation of the real geometry of the axial flow compressor by its plane version is widely used in theoretical models of the gas flow in the molecular pump. To analyze the accuracy of such kind of approaches the numerical algorithm for simulation the free molecular flow in the real geometry of the compressor is developed. The algorithm is based on the well known test particle Monte Carlo method. The pumping process in the considered case is completely characterized by two values of direct and back transmission probabilities. The main problem to be solved during the simulation of molecule motion in the tract is to find the point of intersection of their trajectory, which represents a straight line, with stationary or moving surfaces of the compressor units, where the diffuse-specular reflection of molecule with some accommodation coefficient is assumed. Two types of molecular pump are considered: the Holweck pump with spiral grooves placed on the rotor, and the multi-stage turbomolecular compressor with flat-plate blades. The results obtained for real geometry demonstrate higher compression ratio and are in better agreement with available experimental data in comparison with those obtained for plane version of geometry. The difference between two approaches is higher for higher rotor speed. The main reasons for such difference are the topology of axial flow and non-inertial character of rotating system of reference. The developed algorithm may be used to optimize the design of compressor operating in the free molecular conditions.