In mail, when you are in a specific mailbox, on the top right side of the left hand column (in portrait view) next to "inbox" press "edit". Then in the bottom left corner there is a "mark all" option. You can do that and the unselect what you want to keep.
The other option, if you don't like those red numbers over the mail app is to follow these directions:
settings > notifications center > mail > select the desired mail account if you have more than one and then turn off "badge app icon"
this works for any app that has those (sometimes annoying) red icons. If you don't want that large number of unread emails on your mail app, use this method. If you want to delete them, use the previous suggestion.
Hope this helps!
iPad 3- iOS 7.1.2
iPhone 5S- iOS 7.1.2
iMac 21.5"- late 2013
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