MFT file transmit

You can use EnableSsl of FtpWebRequest to satisfy the encryption requirement of MFT.

http://stackoverflow.com/questions/1534908/transfer-files-over-ftps-ssl-tls-using-c-net

And then you need a remote FTP that supports FTP/S and authenticate against LDAP/AD, and generates log for file upload/download, also remember that the file system on both side must have encryption enabled (might use BitLocker or TrueCrypt).

Although not explicit requirement of MFT, security audit will usually require your server to set "Clear Page File on Shutdown" policy. Some may even require you to use 3rd party software to purge the disk region multiple times on shutdown.

Actually, I think there's a lot of requirement that you need a set of program, not single program, to implement MFT.