1. A method for annotating a three-dimensional page of a three-dimensional electronic document, comprising: displaying the three-dimensional page, the three-dimensional page having a first layer intrinsic therewith; receiving, via an annotation tool, an indication of an area of the object to be annotated; annotating a second layer, the second layer intrinsic with the three-dimensional page by marking the area of the three-dimensional page specified by the annotation tool, the second layer being represented by a three-dimensional geometry; and displaying an annotation corresponding to the specified area, wherein the annotation of the second layer is transformed to and displayed in a third layer other than the second layer and the first layer, the third layer being represented in a two-dimensional coordinate system of the three-dimensional page.