Hi Bryan Yes, both the physical and virtual FD MTUs are separate from each other.  I can change one FD MTU and it will not affect the other.  I changed the physical MTU and it did not modify the virtual.  I also changed the virtual FD MTU and it did not change the physical FD MTU. So, from a GUI standpoint, you can do what you originally asked.  
Hi I would like to know is it possible to have a Physical Fault domain with a different MTU as a Virtual Fault domain that shares the same ports.  According to what I see in DSM config options it "seems" possible.  But would like to know if anyone has done this.  The reason is that I need a different MTU for replication to a DR site, but do not have any additional free physical NICs to create a new dedicated physical fault domain. Currently I have two physical fault domains with 4 ports each. So the plan is to "steal" all physical ports from one of the current fault domains, and create two new fault domains from them: one virtual, one physical, each using the same physical ports (but different vlan tag for each fault domain, and different MTU - one standard frames, one jumbo).   The physical one would be for the new replication traffic (MTU 1500) and the virtual one would be used as a standard front-end I/O fault domain (MTU 9000) I asked copilot a while back and presented my plan to them; they basically said "it should be possible", but that's not overly convincing.  A little disappointing to be honest from supposedly the best support around. Thanks all
Fault domain MTU question