A method and apparatus for segmenting geobodies extracted from three-dimensional geophysical survey data volumes. In one embodiment, the invention involves (a) obtaining a plurality of data elements, respectively corresponding to three-dimensional locations in a subsurface region, and generating a data volume consisting of discrete cells from the plurality of data elements (1); (b) identifying an initial geobody corresponding to a potential hydrocarbon reservoir within the data volume by grouping cells in the data volume according to a selected connectivity criterion (2); (c) selecting a rule (3) that characterizes stratigraphically reasonable geobodies (e.g. they cannot vertically overlap); and (d) in response to a determination that the initial geobody does not conform to the rule, segmenting the initial geobody into a plurality of fundamental geobodies via processing the data elements with an automated segmentation routine, wherein the fundamental geobodies each conform to the rule (4).