You should be able to find the code that generates your top navigation menu in your header.php theme file (look for wp_list_pages()).
To specify which Pages appear in this menu and which don't, you can either exclude those that you don't want (and all others will show) or include those that you do want (and all others won't show).
To exclude Pages 1, 2, and 3 you would add "&exclude=1,2,3" to the wp_list_pages parameters, so wp_list_pages('title_li=&sort_column=menu_order') in your header.php file would become wp_list_pages('title_li=&sort_column=menu_order&exclude=1,2,3').
To include Pages 1, 2, and 3 you would add "&include=1,2,3" to the wp_list_pages parameters, so wp_list_pages('title_li=&sort_column=menu_order') would become wp_list_pages('title_li=&sort_column=menu_order&include=1,2,3').
- Tim