This paper presents the first segmentation operation defined within the 3D topological map framework. Firstly we show how a traditional segmentation algorithm, found in the literature, can be transposed on a 3D image represented by a topological map. We show the consistency of the results despite of the modifications made to the segmentation algorithm and we study the complexity of the operation. Lastly, we present some experimental results made on 3D medical images. These results show the process duration of this method and validate the interest to use 3D topological map in the context of image processing.