For the stability of offshore structures, such as offshore wind foundations, extreme wave conditions need to be taken into account. Waves from extreme events are critical from the design perspective. In a numerical wave tank, extreme waves can be modeled using focused waves. Here, linear waves are generated from a wave spectrum. The wave crests of the generated waves coincide at a preselected location and time. Focused wave generation is implemented in the numerical wave tank module of REEF3D, which has been extensively and successfully tested for various wave hydrodynamics and wave-structure interaction problems in particular and for free surface flows in general. The open-source CFD code REEF3D solves the three-dimensional Navier-Stokes equations on a staggered Cartesian grid. Solid boundaries are taken into account with the ghost cell immersed boundary method. Higher order numerical schemes are used for time and spatial discretization. The free surface flow is solved as two-phase fluid system. For the interface capturing, the level set method is selected. The level set function can be discretized with high-order schemes. In order to test the generated waves, the time series of the free surface elevation are compared with experimental benchmark cases. The numerically simulated free surface elevation shows good agreement with experimental data. In further computations, the impact of the focused waves on a vertical circular cylinder is investigated. Free surface flow features during the interaction of focused waves with a cylinder are also investigated along with the numerically captured free surface.