find below line in .htaccess
# These lines rewrite /index.php/admin to /admin.
RewriteCond %{REQUEST_URI} ^/index.php/admin.*$
RewriteRule ^index.php/admin(.*) /admin$1 [R]
follow below code for remove index.php
example1= www.domain.com/index.php/affiliate/
# These lines rewrite /index.php/affiliate to /affiliate.
RewriteCond %{REQUEST_URI} ^/index.php/affiliate.*$
RewriteRule ^index.php/affiliate(.*) /affiliate$1 [R]
example2
# These lines rewrite /index.php/articles to /admin.
RewriteCond %{REQUEST_URI} ^/index.php/articles.*$
RewriteRule ^index.php/articles(.*) /articles$1 [R]
# These lines rewrite /index.php/admin to /admin.
RewriteCond %{REQUEST_URI} ^/index.php/admin.*$
RewriteRule ^index.php/admin(.*) /admin$1 [R]
follow below code for remove index.php
example1= www.domain.com/index.php/affiliate/
# These lines rewrite /index.php/affiliate to /affiliate.
RewriteCond %{REQUEST_URI} ^/index.php/affiliate.*$
RewriteRule ^index.php/affiliate(.*) /affiliate$1 [R]
example2
# These lines rewrite /index.php/articles to /admin.
RewriteCond %{REQUEST_URI} ^/index.php/articles.*$
RewriteRule ^index.php/articles(.*) /articles$1 [R]