In your Loop, whether for a ‘single’ page or an ‘index’ page, check the post author against the current user ID, and only display the post if they match. Assuming you are using a typical WordPress Loop, something like…
global $current_user;
get_currentuserinfo();
// start of the Loop
if ( have_posts() ) {
while ( have_posts() ) {
the_post();
if ($post->post_author != $current_user->ID) continue;
This also assumes that you are inserting your Custom Post Type entries correctly so that all of the data is populated as it should be.