In order to estimate the multi-layer surface profile and to detect the inter-layer surfaces defects, gated wavefront sensing approach has been proposed in the previous works [1,2]. However, the proposed methodology measures the wavefront that has been distorted by its prior surfaces (reflected wavefront) or post surfaces (transmitted wavefront). Analysis has to be performed to estimate the multi-layer wavefront sensing by taking into consideration the multi-layer surfaces condition. For reflected wavefront, the bottom layer(s) wavefront is (are) being distorted twice via separate interface points while traveling back to the lenslet arrays through our observation for the slope and phase measurement. The subsequent reconstructed surfaces are not accurate and corrected. Thus, a discrete layer correction technique for the surface reconstruction has been proposed to enhance the reconstruction accuracy by using the upper/top layer's wavefront information. This paper discusses on the case of 2-layer system, where the reflected wavefront from the bottom layer has been distorted and its surface reconstruction has been corrected. The results show that the distortion is significant and the correction is deemed necessary for industrial application such as in wafer warpage inter-layer profile estimation.