1. An endoscope system comprising: an insertion portion that is inserted into a subject; an objective optical window that is provided on a distal end side of the insertion portion and receives light from the subject; an image pickup section that picks up an image of an inside of the subject from the light entering from the objective optical window; a position information acquiring section that acquires position information of the objective optical window; an alignment section that aligns the position of the objective optical window acquired from the position information acquiring section with a reference position of a predetermined organ in the subject in a coordinate system of a three-dimensional model image based on an amount of change of subject internal image information inside the subject, predetermined operation input or the position information with respect to a preset reference plane; and an image generating section that generates an image with a subject internal image pasted onto a two-dimensional model image of the predetermined organ obtained by two-dimensionally developing the three-dimensional model image in which the position of the objective optical window is associated with a reference position in the coordinate system by the alignment section, wherein the position information acquiring section acquires direction information in addition to the position information and further comprises a shape estimation section that performs shape estimation of the insertion portion based on the position information and the direction information, and the image generating section superimposes shape information estimated by the shape estimation section on the three-dimensional model image relating to the predetermined organ.