It is possible depending on the configuration of you're filer. One thing to check is that the :
options cf.giveback.auto.enable
is set to "Off" so that when you're first upgrade node reboots, it doesn't automatically take back it's resources.once the first node is upgraded successfully, you can use the "CF Giveback" command to fail back over. Then repeat the steps to Takeover the resources from the 2nd Node in order to upgrade the 2nd node.
Another way would be to arrange an outage window and disable the cluster (cf disable) while you upgrade each node, but that can be a pain depending on what you are using the Filers for.
There may be other things to watch out for depending on the Filer model, configuration, version of ONTAP etc. If you are unsure in anyway, I would contact Netapp.