Orography presents significant modifications to the flow, and terrain complexities that include slopes, valleys, canyons, escarpments, gorges and bluffs span different space-time scales, contributing to a host of phenomena that stymie the predictability of mountain weather. The Advanced Research version of the Weather Research and Forecasting (WRF) system was used to investigate the ability of a leading edge mesoscale atmospheric model to predict key atmospheric phenomena observed during the Mountain Terrain Atmospheric Modeling and Observations (MATERHORN) field campaigns. The WRF simulations were run with a 0.5 km horizontal grid resolution for selected Intense Observations Periods (IOPs). The research described in this thesis is focused on periods of synoptically driven stably stratified atmospheric boundary layers. This work aims to evaluate the performance of the WRF model to simulate real atmospheric conditions and investigate flow passing over a non-symmetrical rugged obstacle. The known theories for stably stratified flow features were found to be too restrictive for complex terrain in point, and a numerical approach was applied. A challenge is that vector fields describing the flow are fully 3D and thus streamlines are not restricted to a single fixed 2D plane, causing presentational difficulties. To this end, a special system of visualization programs was developed, capable of tracking the energy budget and pressure anomalies or analyzing 3D WRF variables along a streamline. Such tools provided an exceptional opportunity to investigate different phenomena related to real complex terrain, which includes the dividing streamline height and flow separation, trapped lee waves, and vortex formation. A selected set of phenomena were investigated, focusing on flow patterns and underlying physics and dynamics.