We have developed an efficient virtual dissection tool to create generic 3D models for anatomical atlases without the need for artistic drawings. Our custom-developed tool can be used to extract 3D models from 2D medical image stacks, cut the models and align the sub-models. Corresponding 2D medical image portions of the sub-models can then be registered and averaged. In the end, a generic model can be obtained from the averaged 2D images of several subjects. The technique optimizes the functionalities of existing toolkits and the resulting software package will allow biologists to build their atlases more quickly and accurately.