Fast and accurate 3D object reconstruction from 2D image slices represents a difficult and challenging problem. Scientists have to either manually define the boundary of the partial object which is time consuming and may lack accuracy or provide the object boundary data which requires all objects be segmented. In this paper, we propose a new method for 3D reconstruction based on optimal image contour mapping. We also propose a novel date structure to represent the corresponding 3D objects. In our approach, all object contours in the same slice as well as adjacent slices are automatically segmented and combined in a hierarchical tree data structure. This data structure allows fast 3D object retrieval and 3D component analysis.