Purpose: This technical note describes the physical and numerical considerations for developing an idealized numerical wave-structure interaction modeling study using the fully nonlinear, phase-resolving Boussinesq-type wave model, FUNWAVE-TVD (Shi et al. 2012). The focus of the study is on the range of validity of input wave characteristics and the appropriate numerical domain properties when inserting partially submerged, impermeable (i.e., fully reflective) coastal structures in the domain. These structures include typical designs for breakwaters, groins, jetties, dikes, and levees. In addition to presenting general numerical modeling best practices for FUNWAVE-TVD, the influence of nonlinear wave-wave interactions on regular wave propagation in the numerical domain is discussed. The scope of coastal structures considered in this document is restricted to a single partially submerged, impermeable breakwater, but the setup and the results can be extended to other similar structures without a loss of generality. The intended audience for these materials is novice to intermediate users of the FUNWAVE-TVD wave model, specifically those seeking to implement coastal structures in a numerical domain or to investigate basic wave-structure interaction responses in a surrogate model prior to considering a full-fledged 3-D Navier-Stokes Computational Fluid Dynamics (CFD) model. From this document, users will gain a fundamental understanding of practical modeling guidelines that will flatten the learning curve of the model and enhance the final product of a wave modeling study. Providing coastal planners and engineers with ease of model access and usability guidance will facilitate rapid screening of design alternatives for efficient and effective decision-making under environmental uncertainty.