I've completed upload scripts similar to this many times before for use on my own webservers. I can complete this project easily with PHP and MySQL. I will provide a simple, non-styled, working version of the script. If you require a nice-looking website, I will have to increase my bid.
What exactly do you mean by "it will create another subdir"? Should each file be placed in its own subdirectory on the server? It would be much easier to simply store the files in MySQL and access them with an ID number provided by the link. But, if you'd rather have each file stored in a subdirectory, I can do that very easily.