Not manually, the non-SEF URL should be automatically redirected to correct SEF one, if you have the "Redirect nonSEF URLs to SEF" option enabled in JoomSEF's Configuration on the Advanced tab.
So your website wasn't indexed before you installed JoomSEF? In that case non-SEF URLs shouldn't get indexed by Google. Try checking the webmasters tools if you can find on which pages it found them and check those pages if they really contain the non-SEF URLs. Or just check your website's source code if the non-SEF URLs are present there somewhere.
Demoting non-SEF URLs probably won't help, as it only affects the Sitelinks, see:
support.google.com/webmasters/bin/answer...=en&answer=47334