Nanowires show a large potential for various electrooptical devices, such as light emitting diodes, solar cells and nanowire lasers. We present a method developed to calculate the modal reflection and transmission matrix at the end facets of a waveguide of arbitrary cross-section, resulting in a generalized version of the Fresnel equations. The reflection can be conveniently computed using Fast Fourier Transforms, once the waveguide modes are known. We demonstrate that the reflection coefficient is qualitatively described by two main parameters, the modal field confinement and the average Fresnel reflection of the plane waves constituting the waveguide mode.