Restoring the ubuntu instalation USB to usable format

You cannot format the bootable usb / startup disk that you create for ubuntu using the linux or windows gui.
I have found the solution from this page works.
https://dottheslash.wordpress.com/2011/11/29/deleting-all-partitions-on-a-usb-drive/

You have to delete the partition one by one and finally format the whole usb drive.

Due to my rampant experimentation with many different Linux distros, I often times have to wipe a USB drive completely after making it a bootable live USB for something like OpenSUSE. If you used the Imagewriter.exe program used to create the drive, you’ll have a hard time later on if you try to use uNetBootin to make a live USB for a different distro. You can use bootice.exe in Windows to restore the drive. Here’s how to do it with fdisk in Linux (courtesy of PenDriveLinux.com)Restoring your USB key to it’s original state using Linux:

First we need to delete the old partitions that remain on the USB key.

1. Open a terminal and type sudo su
2. Type fdisk -l and note your USB drive letter.
3. Type fdisk /dev/sdx (replacing x with your drive letter)
4. Type d to proceed to delete a partition
5. Type 1 to select the 1st partition and press enter
6. Type d to proceed to delete another partition (fdisk should automatically select the second partition)

Next we need to create the new partition.

1. Type n to make a new partition
2. Type p to make this partition primary and press enter
3. Type 1 to make this the first partition and then press enter
4. Press enter to accept the default first cylinder
5. Press enter again to accept the default last cylinder
6. Type w to write the new partition information to the USB key
7. Type umount /dev/sdx (replacing x with your drive letter)

The last step is to create the fat filesystem.

1. Type mkfs.vfat -F 32 /dev/sdx1 (replacing x with your USB key drive letter)

That’s it, you should now have a restored USB key with a single fat 32 partition that can be read from any computer.