Putty is your SSH client to talk to your server. What you need to do depends on what software your server is running (not on the software you use to send commands to the server). There are a lot of possible ways a server could be set up, and a lot of possible ACME Clients that it could be using. There are instructions for many of the common ones linked in the second post of this thread, but if you don't know what software it's running then we probably don't either. 
Hope that helps.
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