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 the 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 the position in the coordinate system by the alignment section.