A user-friendly way of cloning a git repo is through the eGit plug-in in Eclipse. But sometimes, especially on Windows machines, Eclipse has trouble cleaning up after itself after completing a clone operation. The best workaround for this is to clone the repo from git bash and then import the repo in Eclipse.
default@ZDOMINGUEZ-T420 ~
$ git clone git@github.com:<your git repo> <local folder to check out to>
When git finishes cloning your repo, import it to Eclipse.
Browse to the folder you checked out to, click OK, and the newly-cloned repo should now appear on the Git Repositories view.