Three dimensional modeling for seafloor topography is essential to monitoring displacements in underwater structures as well as all sorts of disasters along the shore. MBES is a system that is capable of high-density water depth measurement for seafloor topography and is in broad uses for gathering 3D data and detecting displacements. MBES data, however, contain random errors that take place in the equipment offset and surveying process and require systematic researches on the correction of wrong depth measurements. Thus this study set out to propose a post-processing technique to eliminate an array of random errors taking place after equipment offset correction and basic noise correction in the MBES system and analyze its applicability to seafloor topography modeling by applying it to the subject area.