A three-dimensional object printer generates image data of an object being formed in the printer with an optical sensor and identifies the heights of object features above a substrate on which the object is being formed. A controller operates one or more actuators to move the optical sensor at a plurality of distances above the object to generate image data of the object at a plurality of heights above the object. The controller identifies the distances of the features of the object with reference to the image data generated by the optical sensor and the focal length of the optical sensor.