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Ashjuk, yes it's true that Calibre organises the files and folders in its own way. However, the idea behind this is that Calibre builds a database and you interact solely with that and completely ignore the files on the disk. You can assign genres to books within Calibre. The advantage of doing things this way is that one book can come under multiple genres, and you can perform searches and batch operations, etc. These things aren't so easy (and in some cases not possible) with organised directory trees. Calibre isn't seeking to impose its file structure upon you, the structure is just a consequence of it being a database. Of course, if you prefer not to use such software and want to roll your own directory trees then this is fine also.
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