Can I use TreeCopy to copy a web server directory structure?

Yes. This is one of the most common uses of TreeCopy. For example, you can replicate your IIS wwwroot directory structure to a backup location with a single command:

treecopy.exe D:\InetPub\wwwroot\ F:\backups\wwwroot\

This creates an identical folder hierarchy at the destination without copying any of the actual web files.