FUSE is designed to operate on filesystems in userspace - it says nothing about creating the filesystem representation on a disk the first place - and this would be outside the scope of FUSE - you just use regular utilities.
As it would be a one of, I would expect you would simply use the appropriate mkfs tools (if they exist). So for NTFS you might use mkfs.ntfs or mkntfs (depending on distro, version etc) - ie outside of FUSE.
The same would be true of any other filesystem that you could find a way to formaat.