Waveguide systems are known to be the power carriers from the transmitter end to the input of an antenna or receivers in any given communication system handling low loss and high-power signal transmission like the ones for radar equipment. However, the entire waveguide system tends to be constructed using multiple parts or sections performing variety of electrical functionalities while connected through waveguide bends, joints, or twists. Additionally, different signal control components such as directional couplers, circulators, isolators, attenuators, phase shifters, and multiport junctions may end up using waveguide modeling technology to serve the connectivity between these different electrical functionalities at RF frequency ranges. Recently, powder-bed fusion metal additive manufacturing (AM) process has matured as a breakthrough technology for the development of RF and microwave components such as waveguides, filters as well as antennas. Additive Manufacturing of RF Waveguide Components showed several advantages over the traditional/conventional machining process especially when it comes to part weight reduction and design flexibility. Moreover, AM technology helped to facilitate the implementation of monolithic waveguide subsystems, thereby allowing the integration of multiple RF functionalities in a single mechanical part which created an advantageous manufacturing capability enabling the exploration of unique and optimized RF design characterization, as well as assembly consolidation. Lastly, various additive manufacturing techniques proved to be efficient for reproducing repeatable and low-loss waveguide components at microwave and mm-wave frequencies such as the E- & H-plane waveguide junctions. However, the surfaces of these printed parts can be rough due to polishing of irregular waveguide structures, uneven surface coating or corrugation of surface while fabricating the waveguides and that may have a noticeable impact on electromagnetic propagation such as additional loss and dispersion effects, the propagation constant and attenuation constant of the waveguide, and change the cut-off frequency of every waveguide mode. Therefore, it becomes very important to study the effect of surface roughness on electromagnetic wave propagation. The presented work will demonstrate the use of multi-physis simulation-based techniques in the design and optimization of RF waveguide assemblies as well as the impact of surface roughness introduced by 3D printing process on the RF performance of the waveguide structure. Both thermal & structural geometry deformation are also evaluated for design reliability and electro-thermal management. Authors will demonstrate the usability of simulation-based products for high frequency performance and additive process optimization. Simulations of design iterations significantly reduce the risk of manufacturing failure and help get product to the market quicker. The consolidated waveguide monolithic may have sub-optimal surface roughness. The simulation can account for surface roughness issues while predicting RF performance. Post-processing for surface roughness can also be optimized using simulation tools. Lastly, the simulation data, additive process and material information can be managed through a common digital thread to provide traceability in a large manufacturing environment. The demonstrated workflow can be generalized to wide variety of radio frequency applications such as phased array antennas with complex feeding networks or multi-beam active antenna array with polarizers, filters, couplers and power dividers.