The planning and realization of wind energy projects requires an as accurate and precise wind resource estimation as possible. Standard procedures combine shorter on-site measurements with the application of numerical models. The uncertainties of the numerical data generated from these models are, particularly in complex onshore terrain, not just rather high but typically not well quantified. In this article we propose a methodology for using a single scanning Doppler wind lidar device to calibrate the output data of a numerical flow model and with this not just quantify but potentially also reduce the uncertainties of the final wind resource estimate. The scanning lidar is configured to perform Plan Position Indicator (PPI) scans and the numerical flow data are projected onto this geometry. Deviations of the derived from the recorded line-of-sight wind speeds are used to identify deficiencies of the model and as starting point for an improvement and tuning. The developed methodology is demonstrated based on a study for a site in moderately complex terrain in central Germany and using two rather different types of numerical flow models. The findings suggest that the use of the methodology and the introduced scanning wind lidar technology offers a promising opportunity to control the uncertainty of the applied flow models, which can otherwise only be estimated very roughly.