A three-dimensional model Mixfor-3D of soil–vegetation–atmosphere transfer (SVAT) was developed and applied to estimate possible effects of tree clear-cutting on radiation and soil temperature regimes of a forest ecosystem. The Mixfor-3D model consists of several closely coupled 3D sub-models describing: forest stand structure; radiative transfer in a forest canopy; turbulent transfer of sensible heat, H 2O and CO 2 between ground surface and the atmospheric surface layer; evapotranspiration of ground surface vegetation and soil; heat and moisture transfer in soil. The model operates with the horizontal grid resolution, 2 m × 2 m; vertical resolution, 1 m and primary time step, 1 h. The model was tested against meteorological data obtained at a small clear-cutting area in Otterbach in central Germany during summer 2005. The meteorological data including air temperature and humidity, precipitation, solar radiation, wind speed and direction, soil temperatures at 10 and 20 cm depth were measured by five automatic stations within the clear-cut area. One reference station was placed about 100 m from the clear-cut inside the forest stand. Comparisons of modelled and measured solar radiation fluxes and soil temperature profiles showed that the model adequately describes the spatial heterogeneity and dynamics of these variables under different weather conditions. The model can be used to explore solar radiation and soil temperature patterns within heterogeneous forest plots, with applications to various silvicultural tasks.