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The effectiveness of content-based image retrieval can be enhanced using heterogeneous features embedded in the images. However, since the features in texture, color, and shape are generated using different computation methods and thus may require different similarity measurements, the integration of the retrievals on heterogeneous features is a nontrivial task. We present a semantics-based clustering and indexing approach, termed SemQuery, to support visual queries on heterogeneous features of images. Using this approach, the database images are classified based on their heterogeneous features. Each semantic image cluster contains a set of subclusters that are represented by the heterogeneous features that the images contain. An image is included in a semantic cluster if it falls within the scope of all the heterogeneous clusters of the semantic cluster. We also design a neural network model to merge the results of basic queries on individual features. A query processing strategy is then presented to support visual queries on heterogeneous features. An experimental analysis is conducted and presented to demonstrate the effectiveness and efficiency of the proposed approach.