The Terahertz time-domain spectroscopy in re ection mode geometry provides valuable surface and subsurface information, making it suitable for layer analysis, coating, and non-destructive testing applications. The exchanging of position of sample and reference introduce a phase error when the position or alignment of the sample is not exactly maintained during measurements. This micrometre order of pitch error ( Δx) between the reference and the sample could lead to introduce inherent error in the phase spectrum of the sample. In the present work, a new novel approach based on cross-correlation technique has been demonstrated to solve the uncertainty in phase and to reveal the hidden characteristic features of the given sample in THz TDS spectroscopy. We illustrated and demonstrated the advantage of our approach by measuring the optical properties of Te on and RDX by correcting misalignment of 31.5 and 41.4 µm range, respectively.