Eddy current testing is a non-destructive technique, which is widely utilized to detect and monitor degradation and flaws such as cracks in the steam generator tubes located in nuclear power plants. Typically, the analysis of eddy current testing data of steam generator tubes is complex due to the presence of noise sources in the data. These noise sources decrease the signal to noise ratio, and therefore, the detection of flaw signals becomes a difficult task. A signal processing technique has been proposed in this study, which utilizes the Weighted Multipoint Interpolated Discrete Fourier Transform algorithm iteratively, to reduce low frequency sinusoidal noise as a noise source. The performance of the proposed algorithm was assessed based on the noise level, and the flaw signal power. It has been shown that the algorithm effectively estimates the parameters of sinusoidal noise, and improves the signal to noise ratio of the flaw signals.