An annotation method for a three-dimensional model is disclosed. A first set of data representative of a three-dimensional model is stored in a computer memory. A second set of data representative of an annotation is also stored in the computer memory. The annotation is associated with a first spatial location on the three-dimensional model and a first display view. The three-dimensional model and a first graphical representation of the annotation is displayed according to the first display view, with the annotation being positioned as specified by the associated first spatial location. The displaying of the three-dimensional model is modified to a second display view different from the first display view. The annotation is removed from the display window, and an annotation indicator associated with the annotation is displayed. The annotation indicator is visible independent of any display view of the three-dimensional model.