How about using SEO SpyGlass for that? There is an option in File -> New Project Expert options -> Import Google Webmaster backlinks. Once you import the Google Webmaster tools csv file with backlinks you can login to your Google Analytics account in Preferences -> Google Analytics account and get the visits number for all the backlinks.
This way you will import only the links that brought you some traffic, and will have a picture of your traffic at hand. Please let us know if that does what you need.