URL and .htaccess

I want clear url for SEO point of view. i have changed and added the following .htaccess code and configuration in main.php
//.htaccess:
======================

IndexIgnore */*
RewriteEngine on

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

RewriteRule . index.php

=================================

//main.php
====================================
'urlManager' => array(

'urlFormat' => 'path',
'showScriptName' => false,
'rules' => array(
'<controller:\w+>/<id:\d+>' => '<controller>/view',
'<controller:\w+>/<action:\w+>/<id:\d+>' => '<controller>/<action>',
'<controller:\w+>/<action:\w+>' => '<controller>/<action>',
),
),
=====================================

this issue is i have a number of links in my application with ?r=controller/method how can i handle it with .htaccess without changing all the URLs format in my application.

Thanks in advance