Multiple object segmentation is performed for three-dimensional computed tomography. The adjacent objects are individually segmented. Overlapping regions or locations designated as belonging to both objects may be identified. Confidence maps for the individual segmentations are used to label the locations of the overlap as belonging to one or the other object, not both. This re-segmentation is applied for the overlapping local, and not other locations. Confidence maps in re-segmentation and application just to overlap locations may be used independently of each other or in combination.