Can you be more specific about what you want to build? Are you asking us how to build a FTP server using C#? Are you looking to build a C# application that will FTP to a server?
The combination of "FTP ... with webservices" simply doesn't go together. You can use FTP, or you can build a web service that will accept data, but the two don't relate.
If you want to allow your users to upload large files using FTP, I'd recommend just setting up an FTP server. There are plenty out there, and most web hosts already have it set up. There isn't much point in building one.
In general, it's not much use asking these forums for complete solutions. (Unless, as many people note in their signatures, you want to hire someone to write something for you.) You are much better off asking a specific question about a specific problem.