This paper proposed context based annotation model and annotation ambiguity correction methods. The proposed model provides various annotation types, semantic models, and pen-based free drawing interface. Annotation correction method that is specifically based on the context which includes various textual and structure information between free-form marking and annotation. Also, interface for XML environment using the proposed model and correction methods is proposed and possibilities of application is looked at. The results from the implementation of the proposed method show that the annotated areas included in the free-form marking information are more accurate, achieving more accurate exchange results amongst multiple users in a heterogeneous document environment