Hi, and welcome to MobileRead!
This is a topic that's arisen a number of times, and the simple answer is you can't - Calibre doesn't work that way.
What's a meaningful structure for you (or me, or virtually anyone else) isn't the best way of storing things in a database (which is what Calibre is). Calibre takes its own copy of any books added to its library and stores them to suit its purposes.
Calibre does not refer to your original copy, so you can still do whatever you like with that.
Calibre is a book management system, and does things differently to you (or me) using a file system. Give it a chance and you'll probably find that it does what you want (and more besides).
Good luck!
P.S.
I love the quote from Worldwalker's signature on this topic:
"Filesystems manage files. Calibre manages books. Let calibre do what it's there for, and don't go peeking up its skirt. It'll slap you."
Last edited by mediax; 10-28-2010 at 11:40 AM.
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