1) store the pdf files outsite of the web server root directory
2) use sessions or some other method to verify if the user is logged on. send back a html page with a list of pdf files to view/download if the user is logged on with a link to another page ("pdfdownload.php?filename=test.pdf").
3) have pdfdownload.php check to see if the user is logged in. if the user is logged in and request a file, clean up the $filename (as not to allow the user to request /etc/passwd) then set headers and send the file using fpassthru().
you might want to use a database to store the file information and local file path.