A sequence in the earth, defined by an upper sequence boundary and a lower sequence boundary, where at least one of the boundaries includes an unconformity, is modeled by creating a restored space corresponding to the sequence by reconstructing a portion of the sequence missing because of the unconformity. The sequence in restored space has a restored top boundary having a position and a restored base boundary having a position. Stratigraphic layering is performed within the restored space sequence, using as guides the positions of the restored top boundary and the restored base boundary of the sequence in restored space.