PuTTY is a ssh client. SSH uses encrypted communication, that's all there is to it.
FTP is not secure. As you want to use putty, I suppose that you also want secure ftp.
You can consider to use vsftpd on the server side. I took the instructions to set it up from http://www.brennan.id.au/14-FTP_Server.html
. Next to the ftp clients that are mentioned in the article, FileZilla (under Windows) and lftp (commandline under Linux) can be used as ftp-clients in this scenario
The site might have other info as well (i.e http://www.brennan.id.au/16-Secure_Shell.html
is a chapter about SSH). I do not use SFTP (that comes with SSHD) as it allows access to all directories on the server (so users can i.e retrieve the password file). By patching SSHD (or maybe a newer version) in combination with a proper setup you can prevent this, but vsftpd was easier (I'm a lazy person). If you don't use SFTP, disable it.
If the webserver needs to be secure (https instead of http), look at http://www.linuxquestions.org/questi...d.php?t=451710
where I posted instructions that got it working on my server.