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Annotations on paper documents include important information. We can exploit the information by extracting and analyzing annotations. In this paper, we propose a method of annotation extraction from paper documents. Unlike previous methods which limit colors or types of annotations to be extracted, the proposed method attempts to extract annotations by comparing a document image of an annotated document with its original document image for removing the limitations. The proposed method is characterized by fast matching and flexible subtraction of images both of which are essential to the annotation extraction by comparison. Experimental results have shown that color annotations can be extracted from color documents.