It depends on what type of storage your server is using. If the setup is already completed and you are using only local SR. you can not convert the format of the disk without reinstalling Xen on the drive. if you do have additional drives, simply fdisk the drive as ext3 (makefs.ext3) then create an SR to use as default.
xe sr-create content-type="Local SR" host-uuid=(press tab to enter it automatically) type=ext device-config-device=/dev/sda(DeviceNumberGoesHere) shared=false name-label="Local File SR"
If you do a clean install of Xen, make sure to choose thin provisioning for XenDesktop. This will default your storage format to ext3
“Important: Thin Provisioning changes the default local storage type of the host from LVM to EXT3”
http://support.citrix.com/servlet/KbServlet/download/32308-102-691301/installation.pdf
Chapter 5. XenServer and IntelliCache
in your nova.conf set the storage to use the default