How to Remove the Index.php From Joomla! Google Webmaster
When Google crawls your website, it attempts to view every page on the site. All of the pages can then appear in Google's search results. If you have a Joomla!-based site with an index.php page, then that page will appear in Google. If you do not want the index.php page to appear in the search results, you can remove it by using the Google Webmaster Tools removal request form.
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Instructions
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Enter your host's file manager or use an FTP client to access your site. Highlight the page name and press "Delete" to delete the index.php page from your Joomla! site.
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Go to google.com/webmasters/tools/removals.
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Click "New Removal Request."
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Type the exact URL of the index.php page, such as "example.com/index.php".
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Click "Continue."
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Check the box next to the line that begins as follows: "For permanent removal."
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Click "Submit Request."
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