The direct ellipse-specific algebraic fitting (DESAF) method proposed by Fitzgibbon is a classical method to fit an ellipse from discrete points. Generally, for a complete spot, an ellipse, which coincides well with the complete contour of the spot, can be fitted by DESAF. However, for an incomplete spot damaged by some noises such as nonuniform optical surfaces, depth steps, and occlusion, DESAF would fit an incorrect ellipse which could not accurately match the complete contour of the spot. We analyze this problem encountered in the onsite three-dimensional measurement of hull plates and propose a method to remove these outlier points from the contours of incomplete spots. The experiments of computer simulated data and real data demonstrate that the proposed method can dramatically remove the outlier points from the contour and improve the detection accuracy of the center of the incomplete spot.