1. A method for annotating a three-dimensional electronic document, comprising: selecting a page of the three-dimensional electronic document to be annotated; providing an annotation tool having a color and an ink density to annotate the selected page; specifying an area, on a two-dimensional screen, of the page to be annotated by the annotation tool; and displaying annotation data corresponding to the specified area, wherein the annotation data of the specified area is stored and correlated with other data of the selected page.