Mst,
Manichean is generally quite knowledgeable, but is incorrect in this instance. I think he was attempting to stop the endless number of "I want to use my own file structure" threads that get started.
You can definitely use and have a
Lastname, Firstname author sort and file structure within Calibre - as managed by Calibre (which is the critical part - see below). However, it's implementation and use is not immediately obvious. It involves altering a Tweak's setting. Please see the thread
"Importing and maintaining title, author" where
chaley explains this exact situation to me.
One thing not mentioned in the other topic, which can be quite annoying, is how non-standard last names (A. E. van Vogt, L. E. Modessitt Jr, etc) appear in folders (van Vogt_ A. E_). Note the use of underscores for any end-of-field symbol. So consider whether you just want the author sort in Calibre to show up as Lastname, Firstname
on the screen or if you also want the
folders and ebook file names to do the same thing. (Especially if you're on Windows 7 since the search & indexing built into the operating system kind of makes doing this moot.)
Otherwise, Manichean is correct in that users should not be manually using or altering any part of the calibre ebook file structure. Doing so will eventually lead to a loss of data when (not "if") a user-error occurs.