I have just successfully formatted a completely blank floppy in a USB drive. This required a proper format, and not just writing a filesystem to the disk, because there were no sectors on it yet.
This is done with the ufiformat program, which is specifically designed to work with USB floppy drives.
$ sudo ufiformat -f 1440 -v /dev/sdd
format on device=/dev/sdd, size=1440
geometry: track=80, head=2, sector=18, block=512
done
This formats a 1.44MB floppy (-f 1440) in verbose mode (-v) using the USB floppy device at /dev/sdd. Use -f 720 for a 720k disk.
Here is some other information I found on my journey:
mkfs.msdos and mformat do not actually format a disk, they simply write a DOS (FAT12) filesystem onto an already formatted disk. If the disk has not been formatted (or has Amiga or other non-DOS data on it) then these programs will fail. You will of course have to use these programs to put a filesystem onto the floppy, after you have formatted it with ufiformat.
Likewise using dd to write an image to the disk won't work until the disk has been formatted first.
fdformat is only designed to work with PC-style floppy controllers (e.g. with drives that plug in to the motherboard floppy connectors.) It is not able to work with USB floppy drives.