A new algorithm for Doppler profile detection of Radar echoes using Matched Filter is developed in this paper. The algorithm is applied to the time series radar data obtained from the mesosphere- stratosphere- troposphere (MST) region near Gadanki, Tirupati Matched filter is often referred to as optimum filter. The most unique characteristic of the matched filter is that it produces the maximum achievable instantaneous SNR at its output when a signal plus additive white noise is present at the input.  This presents a new technique adopted when information regarding all the range bins is available and the processing load can be handled. The results are compared with the traditional FFT technique and are presented for the performance evaluation. The merits and limitations of this method of detecting dopplers in comparison to FFT are discussed.