1. A three-dimensional information processing apparatus generating three-dimensional information on a predetermined area with a terrain model representing a terrain in the predetermined area by three-dimensional coordinates and a structure model representing a structure positioned in the predetermined area by the three-dimensional coordinates, the apparatus comprising: a structure bottom surface range calculator that determines, as a bottom surface range of the structure model, a range including a bottom surface of the structure model; a terrain vertex synthesizer that determines a set of vertices for the terrain model including the bottom surface range of the structure model; a bottom surface intersection point calculator that determines intersection points between segments formed by the set of vertices for the terrain model and outer peripheral segments of the bottom surface of the structure model; an all-point height calculator that determines heights of the terrain model at the intersection points and at a plurality of points constituting the bottom surface of the structure model; a reference height calculator that determines a reference height in three-dimensional information on the predetermined area from the heights of the terrain model; and a structure height corrector that corrects the height of the structure model using the reference height and the heights of the terrain model at the plurality of points constituting the bottom surface of the structure model.