While the use of three-dimensional sonic anemometers for eddy covariance is well established, there remain questions about its deployment and consequent data analysis. Convention has largely accepted that coordinates must be rotated so that the corrected transverse and vertical mean velocities become zero. In non-ideal terrain, a planar fit coordinate rotation is widely accepted. However, if the coordinate system changes through time, such as in a rapidly growing maize canopy, or is affected by the local topography, finding temporally and directionally stable regions for a reference point is crucial for flux estimation. A model-based recursive partitioning (MOB) algorithm is proposed to answer this problem. The algorithm creates individual wind sectors and accounts for temporal or spatially dependent variables that may affect planar fits. A cross-validation fitting procedure of the MOB algorithm has proved crucial in identifying variables that influence the choice among different parametric models, such as day of year, solar altitude, and wind direction. Momentum exchange is the most sensitive to alternative coordinate rotation systems, especially in stable conditions. The MOB methodology would be most useful during these conditions. The analyses presented here show that in quantifying scalar fluxes during the day, especially in the case of sensible heat flux and by extension to evapotranspiration and carbon dioxide exchange, there is little need for coordinate rotation if the sensors were aligned with the vertical parallel to gravity.