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Recently, researchers are paying more attention to 3D model classification due to its useful applications in multimedia, computer graphics, and so on. Although there exist a number of approaches to classify 3D models, few of them consider the prior knowledge during the process of 3D model classification. In this paper, we propose a new framework called knowledge based cluster ensemble which incorporates the prior knowledge of the dataset into the cluster ensemble framework to classify 3D models. The experiments show that knowledge based cluster ensemble framework works well on 3D human head model database.