Why not use a MySQL database? Easier to manage.
But if not, then you can do something like create a directory that contains all the messages, giving each filename an ID, like 1.txt, 2.txt, or something more uncommon so that they are harder to find, like an MD5 hash of the ID number given to the user.
Then to retrieve it, they can type in their ID # into a field and you can grab the file using this:
[php]// $_REQUEST['id'] contains the ID # of the user (he just put it in to find his message
$dir = './messages/';
$message = file_get_contents($dur . md5($_REQUEST['id']));
print $message;
[/php]