In Joomla 3, the default for the urls will contain the domain name slash then index.php then the page name. 

If you want to make it so that the index.php doesn't show up in the url's take these steps:

urlrewriting

In Joomla's Global configuration, On the SITE tab there is a section called SEO Settings. Click the radio button with Yes on Use URL rewriting.

 

Then in your .htaccess for the site add the following lines (if all you see is htaccess.txt - see the note below).

RewriteEngine On
RewriteCond %{REQUEST_URI} ^/index\.php/
RewriteRule ^index.php/(.*) /$1 [R,L]

Note: If you don't see the .htaccess file using an ftp program, your host's cPanel or your host's file management system, you may need to change the settings so that you see hidden files. If you still don't see it, it may be that when Joomla was set up, the htaccess.txt file was not copied and renamed .htaccess.

Make a copy of the htaccess.txt file and name it .htaccess. Open the .htaccess file in a text editor and add the lines shown above.

Depending on your host's settings, if your Joomla site is a subdomain, these steps may not remove the index.php from the url, and may even break your site causing you to see error pages as you navigate. If this happens, you may need to live with the index.php in the URL and select No for URL rewriting.

 

If done properly, even if a link from a search engine or a 3rd party website has index.php in the url - the user should be redirected to the correct page.