This is hardly a database question, but anyway - do you mean stopping them accessing them altogether, or reading the source?
If you've actually got php running on the server then they'll never get to see the script, just the output of the script.
If you want a 'secret' directory where scripts are kept for server admininstration or something then password protect the directory with a .htaccess file - if you've got cpanel then there's probably an option do set it up for you.