Measurement of roughness in tens of microns on the luminal surface of the arterial wall is expected to provide the basis for an extremely early diagnosis of atherosclerosis. We have previously proposed a method for measuring the surface profile with micron-order precision by exploiting the longitudinal displacement due to pulsation and measuring the radial displacement due to surface roughness. This method allows estimation of the surface profile without influence by the region of heterogeneous sound velocity between the carotid artery and the skin. However, since the radial displacement of the carotid artery wall measured by ultrasound is not only due to the surface roughness but also the artery expansion due to pulsation, the latter has to be removed. In the present study, a novel method for locally removing radial displacements due to pulsation is proposed by using the spatial distribution of the pulsation component. The proposed method was verified by using a target consisting of urethane resin with a 10-µm-high sawtooth shape on the surface. The agreement with the actual profile was significantly improved by the proposed method. This result indicates that locally removing the pulsation component by the proposed method is useful for accurately estimating the micron-order surface profile of the arterial wall.