The accurate consideration of propagation losses in arbitrarily shaped waveguide-based structures is studied in this paper. For such a purpose, a software tool based on the perturbation of the boundary conditions on the waveguide metallic walls and on the boundary integral - resonant mode expansion method has been developed. To show the advantages of the proposed technique with respect to the classic power-loss method, the complex propagation wavenumbers of a double ridge and an elliptical waveguide have been first computed and compared with results of a commercial software based on the finite element technique. Next a circular, a sectorial shaped and a triangular shaped waveguide have been considered. Then, a computer-aided design software package based on this modal analysis tool has been applied to predict the propagation loss effects in complex waveguide structures, such as an evanescent mode ridge waveguide filter, a traditional dual mode filter with circular cavities and a twist component for K-band applications.