Depends what your workflow is. If your subtool is dynamesh, you can just turn on the "Group" button in the Dynamesh menu, then use the SliceCurve brush to cut right through it (then regenerate your dynamesh), it'll create two separate meshes (but still one subtool), it's a really quick way to cut off pieces of dynamesh for…
the topology created by close hole isn't really very clean, you might want to regenerate your dynamesh if that's what you're doing. But yeah if you want really precise results, going back to Max/Maya for some clean modeling is proably your best bet... Really depends on the context.