It is necessary to guarantee the accuracy of measuring machines in the manufacturing industry. The 3D optical coordinate measuring systems (hereinafter referred to as “3D optical CMS”) has become increasingly prevalent in industrial applications. The 3D optical CMS comprised a projector and a stereo camera uses point cloud data to accurately measure complex shapes and builds the shapes to be measured using a polygon mesh. However, when using the 3D optical CMS, measurement errors and measurement variabilities can occur owing to the influence of the surface characteristics of the target objects. Therefore, methods to guarantee the measurement reliability of the 3D optical CMS, even under the varying surface characteristics of the target objects, should be developed. The surface characteristics include color, glossiness, roughness, and fluorescence. In this study, the authors focus on surface color and research the measurement errors and the measurement variabilities during the measurements of target objects with different surface colors. Generally, the 3D optical CMS is used with a calibration gauge for performance evaluation and inspection. A datum ball, ball bar, and step gauge are one of the typical calibration gauges. However, these calibration gauges cannot evaluate the influence of the surface color of the target object on the measurement results. To fabricate calibration gauges for different surface colors is difficult, and if calibration gauges with colors are fabricated by painting or processing, characteristics other than surface color cannot be retained. Therefore, this study aims to establish a new evaluation method for evaluating the influence of the surface color and researches the possibility of substituting the reflected light from the surface of the target object (hereinafter referred to as “target object surface”) with light transmitted from a color filter. If the reflected light from the target object surface is substituted with transmitted light from the color filter, users of the 3D optical CMS does not need to fabricate several colored calibration gauges to evaluate the influence of the surface color on the measurement results. To the best of our knowledge, this approach has not been considered in previous studies on the 3D optical CMS. The proposed approach is validated based on comparisons of the measurement results obtained using color scheme cards and color filters.