In this letter, a method for the improved consideration of propagation losses in metallic waveguide structures is presented. The method relies on the perturbation of the boundary conditions on the metallic walls of the waveguides. Following this advanced technique, we are able to compute a complex modal propagation constant, thus avoiding the drawbacks of the classical power-loss method where losses associated to evanescent modes were not taken into account. A Computer Aided Design (CAD) software package based on such a modal analysis tool has been applied to predict the propagation loss effects in a Ka-Band rectangular waveguide filter.