For the accurate creation of annotation information in a free-form annotation environment, the ambiguity that arises in the analysis stage between the geometric information and annotations needs to be resolved. Therefore, this This paper identifies, analyzes, and proposes presents solutions methods for the ambiguity that can occur between free-form marking and various contexts in XML-based annotation environment. The proposed method is based on context which includes various textual and structure information between free-form marking and annotated part. The proposed method show that the annotated portions areas included in the free-form marking information are more accurate, achieving more accurate exchange results amongst multiple users in a heterogeneous document environment. This study can be effectively applied to eLearning, Cyber-Class, and IETM