This paper presents a newly developed 3-D fully nonlinear wave model in a transient curvilinear coordinate system to simulate propagation of nonlinear waves and their interactions with curved boundaries and cylindrical structures. A mixed explicit and implicit finite difference scheme was utilized to solve the transformed goving equation and boundary conditions in grid systems fitting closely to the irregular boundaries and the time varying free surface. The model’s performance was firstly tested by simulating a solitary wave propagating in a curved channel. This three-dimensional solver, after comparing the results with those obtained from the generalized Boussinesq (gB) model, is demonstrated to be able to produce stable and reliable predictions on the variations of nonlinear waves propagating in a channel with irregular boundary. The results for modeling a solitary wave encountering a vertical cylinder are also presented. It is found the computed wave elevations and hydrodynamic forces agree reasonably well with the experimental measurements and other numerical results.