Actually, the best practice for file storage and manipulation through the web is to keep a reference in the database. This allows you to have clear, readable file names while also allowing you to encrypt the actual file (and name itself) and store any additional info you'd like (such as an upload timestamp).

As far as keeping things tidy go, you should also include a "status" with these references inside the DB and set it to FINISHED / COMPLETED / etc. once the entire process is 100% done. Then you can make a separate cleanup routine that runs once every night or something that removes any stray files and cleans up the DB for files that are older than a certain upload timestamp and not COMPLETED.

This is the fastest way of displaying a files in the browser, as well as the cleanest way of keeping your administration.