The effect of three-dimensional plant heterogeneity on flow past a clearing is investigated by means of large-eddy simulation. A detailed representation of the canopy has been acquired by terrestrial laser scanning for a patch of approximately 328 m length and 172 m width at the field site “Tharandter Wald”, near the city of Dresden, Germany. The scanning data are used to produce a highly resolved, three-dimensional plant area distribution representing the actual canopy. Hence, the vegetation maintains a rich horizontal and vertical structure including the three-dimensional clearing. The scanned plant area density is embedded in a larger domain, which is filled with a heterogeneous forest generated by the virtual canopy generator of Bohrer et al. (Tellus B 59:566–576, 2007). Based on forest inventory maps and airborne laser scanning, the characteristics of the actual canopy are preserved. Furthermore, the topography is extracted from a digital terrain model with some modifications to accommodate for periodic boundary conditions. A large-eddy simulation is performed for neutral atmospheric conditions and compared to simulations of a two-dimensional plant area density and an one-year-long field experiment conducted at the corresponding field site. The results reveal a considerable influence of the plant heterogeneity on the mean velocity field as well as on the turbulent quantities. The three-dimensional environment, e.g., the oblique edges combined with horizontal and vertical variations in plant area density and the topography create a sustained vertical and cross-flow velocity. Downstream of the windward forest edge an enhanced gust zone develops, whose intensity and relative position are influenced by the local canopy density and, therefore, is not constant along the edge. These results lead us to the conclusion that the usage of a three-dimensional plant area distribution is essential for capturing the flow features inside the canopy and within the mixing layer above.