I need a font book factory reset & a clean slate

Question

My font book is is a mess!  I have duplicate fonts in about 4 different directories (my fault) and want a fresh start.  I did an "export" of my fonts but I am unsure how to do a factory reset.  I've read the Font Management in OS X doc but am unclear if clearing the cache will bring me back to just the basic system fonts or only clears the history.
Do I need to go in and delete ("file ----> remove font") the fonts in font book one by one and THEN clear the cache before reinstalling the ones I want in the ONE directory folder where I want them to live?  (lesson learned).  I have 1200 (not including the duplicates) fonts that I need to sift through and am looking for the fastest way to do this without losing the key system fonts for Mac, Office 2011 and Adobe CS5 Creative Suite.
Is that amount of installed fonts still manageable with font book or should I be looking at a different font management solultion?  I can't answer that for myself until I make it manageable with only ONE copy of each font   
Thanks in advance for your help!  I promise that I've read through this site and have been googling all day but haven't been sure about resetting the it all back to square one 
Tara

Answer 1

There isn't an easy, singular answer to your question, though it would be fairly straightforward if it weren't for Office. I am curious how you arrived at 4 directories of fonts. There are only three Fonts folders OS X looks at. The ones in the System folder, the main Library folder, and the one in the active user account. Since you shouldn't even be looking in the System folder (if you don't know what you're doing), the only two places you should have any fonts you've added would be the main Library and your account.
Anyway, start by launching Font Book. Delete any Font sets or Library sets you have created. Close Font Book. Create a new folder on the desktop. Call it "mine". Anything you want really, just so it refers to the fonts in your user account. Go to the Fonts folder in your user account and move all fonts out of that folder to the new one on the desktop. Create another new folder on the desktop named "lib". Open the /Library/Fonts/ folder and move all fonts into the second new folder. Both the /Library/Fonts/ folder, and the Fonts folder in your user account should be empty.
Follow the instructions at the bottom of Font Management in OS X to restore all fonts from the Snow Leopard DVD. You will be using Pacifist to restore both the System and Library fonts. When you're done, your fonts will be back to the way the were when you first installed OS X.
From the desktop folder you named "lib". Move Hoefler Text.ttc and STHeiti Medium.ttc to the /Library/Fonts/ folder. Replace the versions you just restored with these newer versions. They were updated in 10.6.5.
Office 2011 installs many newer versions of fonts OS X comes with. Move these fonts from the 'lib" folder into the /Library/Fonts/ folder so you again replace the ones you just restored.
Arial.ttf
Arial Italic.ttf
Arial Bold.ttf
Arial Bold Italic.ttf
Brush Script.ttf
Times New Roman.ttf
Times New Roman Italic.ttf
Times New Roman Bold.ttf
Times New Roman Bold Italic.ttf
Verdana.ttf
Verdana Italic.ttf
Verdana Bold.ttf
Verdana Bold Italic.ttf
Wingdings.ttf
Wingdings 2.ttf
Wingdings 3.ttf
Here's where it gets a bit trickier. Office 2011 also installs a number of old fonts which conflict with the newer .ttf OpenType fonts. Delete these from the "lib" folder on your desktop. Note that they do not have a file extension.
Andale Mono
Arial Black
Arial Narrow
Arial Rounded Bold
Comic Sans MS
Georgia
Impact
Tahoma
Trebuchet MS
Without being able to see what you have left in the "lib" folder, I can't easily say what you can move back into the /Library/Fonts/ folder. So I'll list everything else Office 2011 installs that you can move back in. Office uses many of these for its supplied templates. Cambria is the default font family for Word.
Abadi MT Condensed Extra Bold
Abadi MT Condensed Light
Baskerville Old Face
Batang.ttf
Bauhaus 93
Bell MT
Bernard MT Condensed
Book Antiqua
Bookman Old Style
Bookshelf Symbol 7.ttf
Braggadocio
Britannic Bold
Calibri Bold Italic.ttf
Calibri Bold.ttf
Calibri Italic.ttf
Calibri.ttf
Calisto MT
Cambria Bold Italic.ttf
Cambria Bold.ttf
Cambria Italic.ttf
Cambria Math.ttf
Cambria.ttf
Candara Bold Italic.ttf
Candara Bold.ttf
Candara Italic.ttf
Candara.ttf
Century
Century Gothic
Century Schoolbook
Colonna
Consolas Bold Italic.ttf
Consolas Bold.ttf
Consolas Italic.ttf
Consolas.ttf
Constantia Bold Italic.ttf
Constantia Bold.ttf
Constantia Italic.ttf
Constantia.ttf
Cooper Black
Copperplate Gothic Bold
Copperplate Gothic Light
Corbel Bold Italic.ttf
Corbel Bold.ttf
Corbel Italic.ttf
Corbel.ttf
Curlz MT
Desdemona
Edwardian Script ITC
Engravers MT
Eurostile
Footlight Light
Franklin Gothic Book Italic.ttf
Franklin Gothic Book.ttf
Franklin Gothic Medium Italic.ttf
Franklin Gothic Medium.ttf
Gabriola.ttf
Garamond
Gill Sans MT Bold Italic.ttf
Gill Sans MT Bold.ttf
Gill Sans MT Italic.ttf
Gill Sans MT.ttf
Gill Sans Ultra Bold
Gloucester MT Extra Condensed
Goudy Old Style
Gulim.ttf
Haettenschweiler
Harrington
Imprint MT Shadow
Kino
Lucida Blackletter
Lucida Bright
Lucida Calligraphy
Lucida Console.ttf
Lucida Fax
Lucida Handwriting
Lucida Sans
Lucida Sans Typewriter
Lucida Sans Unicode.ttf
Marlett.ttf
Matura Script Capitals
Meiryo Bold Italic.ttf
Meiryo Bold.ttf
Meiryo Italic.ttf
Meiryo.ttf
Mistral
Modern No. 20
Monotype Corsiva
Monotype Sorts
MS Gothic.ttf
MS Mincho.ttf
MS PGothic.ttf
MS PMincho.ttf
MS Reference Sans Serif.ttf
MS Reference Specialty.ttf
MT Extra
News Gothic MT
Onyx
Palatino Linotype Bold Italic.ttf
Palatino Linotype Bold.ttf
Palatino Linotype Italic.ttf
Palatino Linotype.ttf
Perpetua Bold Italic.ttf
Perpetua Bold.ttf
Perpetua Italic.ttf
Perpetua Titling MT
Perpetua.ttf
Playbill
PMingLiU.ttf
Rockwell
Rockwell Extra Bold
SimSun.ttf
Stencil
Tw Cen MT Bold Italic.ttf
Tw Cen MT Bold.ttf
Tw Cen MT Italic.ttf
Tw Cen MT.ttf
Wide Latin
Anything you have left in the "lib" folder on your desktop will either be duplicates, or fonts installed by other third party apps. That will essentially be true of any fonts you moved out of your user account. I can't tell you which, if any of these, would need to be moved back in. For now, combine the two into a single folder and store them away anywhere not in any of the three Fonts on the hard drive. There will be a bunch of them as CS5 installs a slew of fonts. None of which it needs to operate.
That's as far as I can help with the fonts themselves.
Now open Disk Utility and run a Repair Permissions on your startup drive. Moving the fonts around will cause them to have permissions OS X doesn't like. Mainly just because you moved them back into the /Library/Fonts/ folder and it will want to change the permissions to OS X as the owner simply because of where they are.
Last few things to do.
Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. You can let go of the Shift key at that point.
OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally. This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode.
Next to take care of the System's font cache files.
Close all running applications. From an administrator account, open the Terminal app and enter the following command. You can also copy/paste it from here into the Terminal window:
sudo atsutil databases -remove
Terminal will then ask for your admin password. As you type, it will not show anything, so be sure to enter it correctly.
This removes all font cache files. Both for the system and the current user font cache files. After running the command, close Terminal and immediately restart your Mac.
Last step when back at the desktop. Launch Font Book so it can create a new database based on the fonts currently in the drive's three Fonts folders.
There should be no duplicates. Everything OS X and Office installs will be available.