Detection and analysis of ocean surface phenomena have so far relied on manual analysis of long sequences of satellite images or images produced from the mathematical models. In this paper a technique for the three-dimensional shape analysis and spato-temporall tracking of mesoscale eddies from MICOM dataset is presented. Mesoscale eddies play a strong role in carrying heat poleward. The shape analysis of eddies provides a volumetric estimation which can be further used to determine the heat trapped in eddies. Eddies are detected and the region of swirling currents around the detected center is segmented. Segmented eddies are stacked to generate 3D visualization. A 3D skeleton is obtained with the centroids of all the layers in the segmented eddy and represented parametrically. Coefficients of the parametric representation are used for motion tracking of eddies.