The answer is two-fold:
1) restore your iTunes folder from your backup.
or
2) it's actually COMPLETELY IRRELEVANT what the folder structure in your iTunes Music folder looks like, as the iTunes interface is FAR better at sorting, grouping, searching, and viewing your music than a catch-all file browser like the Windows Explorer or the Finder could ever be. As TETENAL says, it should hardly ever be necessary to access the folder in the Finder at all.