Wind mapping is of utmost importance in various wind energy and wind engineering applications. The available wind atlases usually provide wind data with low spatial resolution relative to the wind turbine height and usually neglect the effect of topographic features with relatively large or sudden changes in elevation. Two benchmark cases are studied for computational fluid dynamics (CFD) model evaluation on smooth two-dimensional (2D) and three-dimensional (3D) hills. Thereafter, a procedure is introduced to build CFD model of a complex terrain with high terrain roughness heights (dense urban area with skyscrapers) starting from existing topography maps in order to properly extend the wind atlas data over complex terrains. CFD simulations are carried out on a 1:3000 scale model of complex topographic area using Reynolds averaged Navier–Stokes (RANS) equations along with shear stress transport (SST) k-ω turbulence model and the results are compared with the wind tunnel measurements on the same model. The study shows that CFD simulations can be successfully used in qualifying and quantifying the flow over complex topography consisting of a wide range of roughness heights, enabling to map the flow structure with very high spatial resolution.