when we create a menu and submenu in wordpress admin programmatically. It creates a duplicate of top menu as submenu.

That's the default behavior, see the $menu_slug documentation for add_submenu_page:

If you want to NOT duplicate the parent menu item, you need to set the name of the $menu_slug exactly the same as the parent slug.

The problem is that putting the same slug merges the callback for the menu and the submenu.

You may need to manipulate the global $submenu variable to achieve your goal, note that I gave a different slug to the submenu:

add_action( 'admin_menu', 'setup_theme_admin_menus' );    

function setup_theme_admin_menus() 

{    

    add_menu_page(

        'Theme settings', 

        'Example theme', 

        'manage_options',   

        'tut_theme_settings', 

        'theme_settings_page'

    );  

    add_submenu_page(

        'tut_theme_settings',       // parent slug

        'Front Page Elements 2',    // page title

        'Front Page 2',             // menu title

        'manage_options',           // capability

        'tut_theme_settings2',      // slug

        'theme_front_page_settings' // callback

    );  

    // REMOVE THE SUBMENU CREATED BY add_menu_page

    global $submenu;

    unset( $submenu['tut_theme_settings'][0] );

}  

Credit goes to - Stack Overflow and Writer Brasofilo