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The Kohonen self organizing map (SOM) is an excellent tool in exploratory phase of data mining. The SOM is a popular tool that maps a high-dimensional space onto a small number of dimensions by placing similar elements close together, forming clusters. When the number of SOM units is large, to facilitate quantitative analysis of the map and the data, similar units needs to be grouped i.e., clustered. In this paper a two-level clustering based on SOM is proposed, which employs rough set theory to capture the inherent uncertainty involved in cluster analysis. The two-stage procedure (first using SOM to produce the prototypes that are then clustered in the second stage) is found to perform well when compared with crisp clustering of the data and increase the accuracy.