In this paper, we propose a novel Carrier Frequency Offset (CFO) estimation and compensation algorithm applicable to Software Defined Radio (SDR). A two stage estimation algorithm has been proposed as a concatenation of two algorithms namely Modified Maximum Likelihood Data Aided (MMLDA) coarse frequency estimation and sample by sample residual CFO estimation. The second stage tracks the residual offset on sample by sample basis for the whole burst without using preamble. Simulation results are given for Stanford University Interim (SUI) channels to demonstrate the effectiveness of the proposed algorithm in multipath fading channel. The proposed algorithm shows better performance than the conventional two stage algorithms, even for large frequency offsets. The proposed algorithm has been implemented in software on TMS320C64x+ Digital Signal Processor (DSP) core and verified by comparing with simulation results.