Well, you could always do what I do and disable automounting, but since most people seem to be unable to live without this hideous device, I guess I had better think up another tactic.
My other suggestion would be this. Go to your file manager (or run the 'mount' command) and find out where your usb device is mounted (it will be /media/something) put that address into the following command:
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sudo lsof +D /media/0FDD-636E/
(The address I typed there is from a usb device I just mounted on my computer - please don't copy it directly - copy the command by all means, just not the address).
If there is no output from that command then there are no open files on that device so it should be safe to remove.
Fujitsu Lifebook AH532 Laptop. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Ubuntu12.10 (Unity), Mint14 (Cinnamon), Manjaro (Xfce).