Font Minor Problem

I was in Font Book, verified all font and have 35 minor issues, yellow question mark. How do I fix them.
It appears all my fonts are in
\Library\Fonts
\System\Library\Fonts
I have no fonts in \User\Name\Fonts but have collections in FontCollection
1. How to I fix the yellow question marks.
2. Hopefully this will fix a word 2008 issue opening up some documents.
Thanks.

Thanks, I will try to remove the microsoft fonts at
/Library/Fonts/Microsoft
From what I read if you doing it in font book will/may remove the wrong one. Since I already "resolved duplicates" from fontbook menu. How do I undo, probably have to uncheck or use from the menu bar. Thinking about it more if I just delete the font from MS, then validate fonts that should get me where I need to be, no bad fonts.
Thanks

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