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It should automatically do that.
Are you running a cloud sync program? If so, you may have ended up with duplicated folders -- calibre moved them, but Dropbox/SkyDrive/Box/Copy.com/whatever restoredthe old versions.
Or storing the library on a NAS? that would prevent calibre from making the necessary changes -- NAS storage is heavily recommended against.
To test, can you try running Library Maintenance from the dropdown under the switch Library icon in the toolbar. Use Check Library. It will go in two stages, the first checks for database errors, the second stage will ask if you want to check that the database matches the actual files/folders. That includes a check for extra files/folders not associated with the database at all.
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