Can you repair your fonts?...

I know this is my fault, but I'm wondering if I can fix it. I'm a graphic designer, and I've always had problems with Helvetica and now Helvetica Nueue because I use them for designing and the OS uses a different version, so I had followed the instructions I found elsewhere to "fix" them, but now I know that I've borked my fonts because I can't read the headers of e-mails, and other things because the system font isn't working.
So, long story short, isn't there a way to re-install the system fonts or something of the kind so that I can go back to how it was. I should also say that I use Font Explorer Pro to manage my fonts.
I'm also inserting a screen capture of what some web sites look like in Safari now because I'm getting a Capital "A" in a box instead of the proper words.
Thanks in advance for your help.
Steph

Kurt Lang wrote:
In order to use the Helvetica fonts you need for your projects (assuming they are not Apple's versions), you simply can't allow Apple's Helvetica fonts to exist in their normal location since you then cannot turn them off.
What you need to do is have Apple's fonts set aside in their own folder, not in any of the Fonts folders, so you can control them.
Not sure what article you found, but the instructions for getting Apple's fonts out of the way are in my article, Font Management in OS X. Remove these fonts from both the /System/Library/Fonts/ folder, and the buried ProtectedFonts folder. Do the protected ones first so they don't automatically replace those in the System's Fonts folder.
Next, you need to get these fonts back onto the hard drive as I noted above. In a generic folder outside of any Fonts folder. For that, you can use Pacifist. Put your Snow Leopard installation DVD in the drive and use Pacifist to extract the various Helvetica fonts to your new folder.
You will need all of these to satisfy Snow Leopard's normal list of fonts:
Helvetica.dfont
HelveticaNeue.ttc
HelveticaLight.ttf
HelveticaLightItalic.ttf
Once you have your folder of Apple's Helvetica fonts set aside, you're ready to continue.
To remove Font Book from the hard drive, follow these steps:
1) Open Font Book, and then its preferences. Uncheck the box for "Alert me if system fonts change". Close the preferences and shut down Font Book. Put the Font Book application in the trash and delete it.
2) Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding it until 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 reset Font Book's database and clear the cache files in your user account. All fonts in the three main Fonts folders (System, Library, your user account) will now be active, regardless of their state beforehand.
3) 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
This removes all font cache files. Both for the system and all user font cache files. After running the command, close Terminal and immediately restart your Mac.
With Font Book completely gone, and all cache files cleared and rebuilt, things should now be displaying correctly.
Hello Kurt!
I have read both your "Font Management in OS X" article and the referenced "Undoing Font Book" (unfortunately, this article only goes as far as Mac OS X 10.5 Leopard and I'm not sure whether everything would be the sam in Mac OS X 10.6.8 Snow Leopard.)
I've followed all the instructions in your article as soon as I've got my new iMac 2.5 GHz Intel a couple of months ago, but some things are not working right with fonts: Working on a QuarkXPress Passport document previously saved, I was unable to use the HelveticaNeue.ttc font that I had used when originally working on the file as QuarkXPress told me the font was missing.
When in Font Book I tried to see what the problem with this font was, it showed conflicts with "multiple copies of this (as well with other) font" which I cannot resolve by clicking on "resolve duplicate font conflicts": it asks whether I "want to disable the selected fonts", which is not what I want. Actually, Font Book tells you that "you can use the Resolve Duplicates command to automatically deactivate the copies not in use."
If I do this, I believe I won't be able to use whichever font so deactivated, or would I?
I launched Font Book, opened its preferences and unchecked both "Alert me if system fonts change" and "Automatic font activation".
I still get alerts such as "Finder requires AppleSymbols font", "Finder requires Aquakana-Bold font", "System font HelveticaLightItalic.ttff has been restored MacOSX needs it to display text onscreen" after either moving to another location or deleting them in preparation for a complete new Font Book reset as explained on your post.
My question is, should I try removing Font Book from the hard drive and replacing it with a fresh copy and, if so should I do it the way you explain on your reply to stephmoreland?
Even though Font Book is a "weak" font manager, I would rather stick with it as I believe it performs for the kind of work I do on my computer.
Thank you so much for your help,
iMac 2.5 GHz, Mac OS X (10.6.8), 4GB DDR3; HP scanner & printer; 2-WF HD's

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