Disable direct access for subdirectory files from root htaccess

Is there a way to prevent direct access for subdirectory files from the main/root htaccess file.

Here is my app structure

index.php
.htaccess
includes
  -classess
      user.class.php
      news.class.php
  -submit
      home_submit.php
      login_submit.php
      signup_submit.php

I don't want the submit directory files to be accessed directly. How can i specify LimitExcept or something else so that it is applicable only to files in submit directory from the main htaccess file.