Optical Coherence Tomography (OCT) imaging is a high-resolution, sub-surface non-invasive imaging technique, using the principle of low coherence interferometry, that has become increasingly popular for various applications for structural and quantitative imaging [1]. Applications for OCT technology have been demonstrated in ophthalmology, dentistry, cardiology/intravascular imaging, endoscopy and intra-operative surgery, and many new applications are being researched. Due to higher sensitivity and faster rate of image acquisition, frequency domain OCT systems are now replacing the first generation time domain systems. These include spectral domain systems, which use a broadband low coherent source with spectrometer and a line scan camera based receive system, and swept source systems, that use wavelength sweeping source with a photo-detector based receive system. Both of these systems require very similar signal processing to recover the desired image from the captured digitized interference or fringe data. © 2011 Copyright SPIE - The International Society for Optical Engineering.