Provided are a method, system, and article of manufacture wherein at least a first zone is maintained in a fibre channel arbitrated loop system, and wherein a plurality of storage devices is included in the first zone. A determination is made that diagnostic operations have to be performed on a storage device that is included in the plurality of storage devices. A second zone is generated, wherein the second zone includes the storage device on which the diagnostic operations have to be performed, and wherein the storage device is removed from the plurality of storage devices in the first zone leaving a remaining set of storage devices in the first zone. Diagnostic operations are performed on the storage device in the second zone while other operations are performed on the remaining set of storage devices in the first zone.