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If you are taliking about the way that books are stored in the Calibre library, then I am afraid you have no control over the naming convention used and cannot change it. It is always tied to the Author and Title fields.
If you export files from the Calibre library, then you can specify the folder/filename naming format to be used.
Having said all that, with the latest 0.7.21 release you should find it easy enough to copy the author-sort field (which is probably already formated as LN, FN) and that will cause the folders to be renamed to match. You might want to also look at Preferences->Advanced->Tweaks for options on how the Author-Sort field should be constructed from the Author field when adding new books.
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