try the following:

# sudo umount /media/[mount point]

for example
# sudo umount /media/disk1

that should unmount, which removes the drive icon from the desktop.
it's then "safe" to disconnect the drive.  however, the mount point
folder in /media (e.g., "/media/disk") will still be there and unusable.
so it is save to remove that directory by using

# sudo rmdir /media/disk[x]

where [x] is the folder if there are multiple media devices connected.
if there was only one device connected, it should be just /media/disk

the next time you plug the media in, it should auto mount normally.

-- 
Mounts external USB hard drive in a different point after resuming sleep
https://bugs.launchpad.net/bugs/230671
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