A cepstrum technique that not only is capable of precise registration of fundus images but also leads to three-dimensional reconstruction of fundus structures with a motion stereo model is presented. The use of cepstrum techniques allows the representation of the three-dimensional features in a quantitative manner that is impossible to obtain from just a stereoscopic view. A geometrical transformation using a set of polynomial functions is introduced. The definition of the two-dimensional power cepstrum and the analytical procedure for obtaining the disparity are shown in detail. A modified time-sequenced stereo model using a matching technique, i.e., the two-dimensional cepstrum, is introduced.