You can use putty to log in to your server and manipulate your files through the command line.
I use this so I can do things like create a back up dump of my MySQL database or create an archive of files. I also use programs like Cyberduck and Filezilla, but I use those to just transfer files between my local machine and the server.
You can download putty, a free open-source client, at the putty web site:
