I don't Under stand you Question completely..,
Here i am providing some information about the communication between Linux/windows called SSH.
SSH is communication protocol which is used to talk with linux environment through the windows..,
here is link for you, for more details;
http://winscp.net/eng/docs/guide_dotnet[
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http://www.google.co.in/#sclient=psy&hl=en&q=ssh+in+c%23&aq=f&aqi=g-c1g-o1&aql=&oq=&gs_rfai=&pbx=1&fp=68659218eb7f0e93[
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You can execute Linux commands also from the SSH.., Send the desired commands/scripts to down the linux PC..,
:rose::rose::rose: