Why Does index.php reappear in url even after removing it via htaccess

My question is that, I have removed index.php in codeignitor 3 via following code in .htaccess

RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond $1 !^(index\.php|assets|robots\.txt)
RewriteRule ^(.*)$ index.php/$1 [L]

but when i redirect from one controller to another index.php reappear in the URL, As far as i am working within same controller it remains hidden.