When creating annotation information in a free~form environment, ambiguity arises during the analysis stage between geometric information and the annotations. This needs to be resolved so that the accurate creation of annotation information in a free-form annotation environment is possible. This paper identifies and analyzes the ambiguities, specifying methods that are tailored to each of the various contexts that can cause conflicts with free-form marking in a XML-based annotation environment. The proposed general method is based on context which includes various textual and structure information between free-form marking and the annotations themselves. The context information used is expressed in XML based DTD, within the paper. The results are printed and shared through a system specifically implemented for this study. 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.