Multiple volumes can be loaded in CTVox. When working with multiple volumes the Volume Manager pane is central to present additional information for each volume. In addition to the visibility of the volume, the volume label, the volume weight and the volume base color, now you can also adjust the cutting/clipping mode: the effect of the cutting/clipping shape can be set per volume to cutting, clipping or neither through the drop down menu, as indicated with the arrow.
The subvolume cutting and clipping functionality allows to assign different opacity and color schemes to subvolumes representing 3D distribution of morphometric parameters across the scanned volume, but also to different parts of the dataset, simply by loading the same volume twice. Some more examples can be found in MN103.