Systems and methods in accordance with the present invention provide freeform annotation techniques designed to make freeform annotations on a digital document more flexible, reliable and presentable on a screen of a computing device. They allow users to markup the document, add comments, and link between annotations, while maintaining the freeform nature of these annotations without constraining the kinds of annotations allowed. These freeform annotations are then unequivocally recognized via a state machine into three groups of annotation marks: anchor, comment, and link, each of which is associated with either part of the digital document or with another annotation mark. In addition, these annotation marks can be repositioned and resized to fit within the display area available on the screen based on the display properties of the screen, thus supporting the natural flow of annotating the document in a freeform manner. This description is not intended to be a complete description of, or limit the scope of, the invention. Other features, aspects, and objects of the invention can be obtained from a review of the specification, the figures, and the claims.