Alice, are you attempting to set the elevation of each slice to one value, and then deactivate elements to mimic elevation differences of geological layers? In 6.1, elements cannot be deactivated, but you can set the permeability and storage of the element to very small values so that the act like an impermeable barrier or block of material. This won't work if the elements you want to "inactivate" are at the top of the model where non-zero recharge (in/out flow) is applied.
Pete