PHP Directory functions, the examples are in there: http://php.net/dir

Also have a look at DirectoryIterator, I posted some info here: http://www.daniweb.com/forums/thread190732.html

I hope it's not a windows server your using because when I attempted to create over 500,000 folders and subfolders with php, it crashed the external hardrive and had to be formatted. I would VERY strongly suggest to use a database instead as it will be faster and may even reduce the load on your server due to the file system lookup.

Site runs on external Linux web server, was thinking about mysql, but we will be putting up approx 400 PDF's a week to server and storing them in a DB might not be the best idea. It is something that i through about, but it will also cause either 1 of 2 things, 1 I have to write a script to take the PDF's from local storage to the mysql db and sort them, or 2 i am going to have to upload them all myself, both of which are less than ideal.

I need to be able to save down a batch of pdf's with the correct naming convention (thats simple) and have them uploaded to the webserver (netdrive) and then a simple query to find the relevant files and display them to the user as a link.