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I agree. Never alter the file structure that Calibre creates and uses.
If you really know what you are doing with your file manager, you can go in and copy the book files to another place on your drive and arrange them any way you want. Safer yet is to "Copy to File" which tells Calibre to copy the book files to another location on your disc. This prevents any accidents from happening should you go into the Calibre Library itself, which you should regard as sacrosanct.
I think, as the poster above notes, that there is a way to direct calibre to create the folder structure you want in the export (I've never done that), but either way, never change the Calibre folders yourself (because they are indexed for speed to allow Calibre to open quickly even with thousands of books and folders, and if you change the folders, the actual files will not be in sync with the index file, and Calibre will get lost - you do not want that to happen).
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