My site uses mod rewrite and the links are all mod rewrite yet it index's the pages with the php variables for example ?view= and not /view/ :/ Any ideas?
I am assuming your pages already were in google with the old style ?view= format. Put some 301 mod rewrite rules in to the newly formatted URLs.
If your pages are already in the index as ?view=, and you just created a mod rewrite rule to point to the new urls, *google will never pick them up*. As long as the ?view= pages do not return 404s or 301s, google has no reason to remove them from the index, and google will not pick up the new urls because they are duplicate content on the same domain. You have to create either 301 redirects (recommended) or 404s for the old urls to remove them from google's index.