How can I connect to UNIX machine and run unix commands from C# code ?

This is how: https://sshnet.codeplex.com[^].

SSH is a network protocol for secure command-line access to a remote system: http://en.wikipedia.org/wiki/Secure_Shell[^].

You can access a shell account, primarily on Unix-like machine, which should, of course, be running appropriate daemon accepting remote connections and supporting this protocol.

—SA