In this work, we present the results of numerical modeling of distribution of the field amplitude inside micron-sized through cylindrical pores in polymer track membranes in the soft X-ray wavelength range 13.5–30.4 nm. The calculations were performed by numerically solving the 3D parabolic equation with a finite-difference method using an exact transparent boundary condition. The dependences of the X-ray transmittivity through a pore on the incidence angle as well as on the pore diameter were computed. For the membranes with some thicknesses and pore diameters, calculated angular dependences of the transmittance are compared with the measurements known from the literature. It is demonstrated that the calculations agree with the measurements if a transition layer on the inner surface of the pores, which accounts for the finite surface roughness, is introduced.