A very flexible and efficient computer-aided design (CAD) tool, specifically suited for advanced comb-line rectangular waveguide filters, is presented in this work. The developed software tool, which makes use of a full-wave analysis technique based on the Boundary Integral—Resonant Mode Expansion method, allows loading the considered comb-line resonators with any number of radially symmetrical partial-height metallic posts. The implemented CAD tool also allows dealing with coupling windows of arbitrary cross-section, thus drastically enhancing the flexibility of the CAD process. The excitation of the analyzed components, which is performed using generalized coaxial probes, has also been integrated in the implemented software tool, thus achieving a full-wave electromagnetic characterization of the whole component. Furthermore, a novel simple procedure to efficiently connect all the obtained wide-band matrices is proposed. To validate the accuracy and efficiency of this novel CAD tool, several new designs concerning advanced band-pass comb-line waveguide filters are presented. The accuracy of the developed CAD tool has been successfully validated by comparing the obtained results with numerical data provided by a commercial tool based on the finite-element method