How to organize web server directories on Linux?

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http://serverfault.com – I'm searching for an easy way to organize web server directories on Linux. Users can use FTP to upload their web pages onto the server. But if they do this, the files are owned by the user themself and the web server can't write to them. I'm searching for a solution that allows users to upload stuff to the server allows the web server to create/delete/manipulate files allows the users to remove the web server's ability to manipulate certain files/directories for additional application security. How would I do this? (HowTos)