You need to look into Access Zones. By default Isilon has one Access Zone called "System". You can create a new access zone, associated it with a SmartConnect subnet. Once you do that then that new access zone has an "visible shares" options where you can select which SMB shares the Access Zone can see.
NFS still must use the System access zone.
I'd also mention the default "System" access zone is uses with the default subnet (subnet0:pool0). Do not remove "System" for subnet0:pool0 until you have assigned another subnet to System, or you will lose SSH and WebUI access.