Irregular volumes within one or more three-dimensional volume datasets are identified and extracted in response to criteria. The processing involves automatically finding a seed voxel or seed cell that meets the criteria and thus belongs to an irregular volume of interest, and then identifying cells related to the seed cell by one or more predetermined relationships that are therefore also to be grouped into that irregular volume. Information, which can be of any suitable type, identifying each such cell as being related to other cells and belonging to an irregular volume is stored in a suitable data structure. The location or similar neighborhood information and other data describing properties or attributes of the identified cell are also stored. Because the irregular volumes are extracted and pre-processed in this manner, operations including rendering them on a display and performing Boolean and arithmetic operations on them can readily be performed.