Depending on which language and protocol you want to use consider the
following

SFTP (FTP over SSH)

http://www.jscape.com/sftp/ (Java classes)

http://www.jscape.com/sshfactorydotnet/ (.NET classes)

FTPS (FTP over SSL)

http://www.jscape.com/sftp/ (Java classes)

http://www.jscape.com/sftpdotnet/ (.NET classes)

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