system("plink $server");
That starts a new interactive shell on the remote system and it just keeps waiting for you to type some command at the console. What you probably want is: 
system "plink $server $cmd";

[download]
BTW, check also Net::SSH2.

In reply to Re: run a perl script on a unix machine from a win machine by salva
in thread run a perl script on a unix machine from a win machine by akrrs7

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