In this paper, we propose a novel framework for segmentation of documents with complex layouts. The document segmentation is performed by combination of clustering and conditional random fields (CRF) based modeling. The bottom-up approach for segmentation assigns each pixel to a cluster plane based on color intensity. A CRF based discriminative model is learned to extract the local neighborhood information in different cluster/color planes. The final category assignment is done by a top-level CRF based on the semantic correlation learned across clusters. The proposed framework has been extensively tested on multi-colored document images with text overlapping graphics/image.