This article introduces a methodology for automatic generation of geometries and meshes for kilometer-scale Atmospheric Boundary Layer (ABL) flow simulations, with topography and elevation. The proposed programmatic (hence automatable) \emph{template morphing approach} facilitates interpolation of scattered point cloud terrain data on a template geometry domain, morphing a high-quality quadrilateral template mesh for the interpolated geometry, and setup as well as execution of Computational Fluid Dynamics (CFD) flow simulation. The proposed method specifically addresses the previously reported problems of sustaining an ABL structure across the simulation domain by imposing the velocity and turbulence properties on all vertical surfaces. We present a validation study for the proposed method on an artificial Gaussian hill terrain. A real-world localized wind forecast application from the Turku Archipelago, Finland, is also presented, using open terrain data from National Land Survey of Finland. Such localized wind forecasts aim to assist ships in autonomous navigation and maneuvering in complex port or fairway environments, which is the motivation for this study.