This paper is focused on the required post processing of Doppler spectra, acquired from a continuous-wave coher-ent lidar at high sampling rates (400 Hz) and under rapid scanning of the laser beam. In particular, the necessary steps followed for extracting the wind speed from such Doppler spectra are presented. A method for determining the background noise spectrum without interrupting the transmission of the laser beam is described. Moreover, the dependency between the determination of the thresh-old of a Doppler spectrum with low signal-to-noise ratios and the characteristics of the wind flow are investigated and a systematic approach for removing the noise is out-lined. The suggested post processing procedures are ap-plied to two sample time series acquired by a short-range WindScanner during one second each.