Abstract—Imaging type two-dimensional Fourier spectroscopy is the wave front-division interferometer which limits the measurement depth into focal plane. This method has shown the potential in many areas such as measurement of biological substances and non-destructive inspections. Presence of noise in the signal may affect the end result of test. This paper proposes the algorithm for improving spectral data by finding low noisy point and filtering them. Cross correlation with median noisy signal is used to find the best signal to be considered. Experiment was conducted for testing fingerprint, alcohol measurement and measurement of ink. Proposed algorithm was conducted for the data obtained from ink measurement.