In Ubuntu, all USB drives, once mounted, are in the
cp /media/your-usb/file-in-usb ~
That copies a file on your USB disk to the user's home directory, assuming the drive is called
your-usb and the file is
I am not sure why you need permissions to copy from the USB to a local file. Maybe you don't have permission to access the USB or you are trying to copy them to a directory where you don't have permissions. I would do this to find the permissions of the files on the USB drive:
ls -l /media/your-usb/
Post the result of this and the directory you are trying to copy the files to.
I don't recommend running the GUI file manager under super user privileges, but this but this is how you would launch Nautilus in root mode: