The Indian MST radar is sited at National Atmospheric Research Laboratory (NARL), Gadanki, Andhra Pradesh. The MST radar is used to study and characterize the dynamic changes of atmosphere in the regions of Mesosphere, Stratosphere and Troposphere (MST). MST radar was developed with an active phased antenna array consisting of 1024 Yagi-Uda antenna elements and operated by a frequency of 53MHz. In this article, we introduce a sparse iterative parameter estimation approachforspectral estimation for the radar data. Separable models occure normally in spectral analysis, like radar signal processing and astronomy applications. We tested the proposed algorithm for the simulated complex signal which may contain more than one frequency component in presence of noise. For simulated signal, the algorithm has proven to estimate the power spectrum at low SNR conditions also. Finaly, The proposed algorithm (PALG) has been applied to MST radar data collected on 9 Feb, 2015 to compute Doppler spectrum. After computing Doppler spectrum and Doppler velocities, the wind parameters like Zonal U, Meridional V and Wind velocity can be calculated from the Doppler velocities. The obtained wind velocity components of the MST radar data is validated through the Global Positioning System (GPS)balloon data.