You can feed data to the remote process using the stdin_data option as follows:

$ssh = Net::OpenSSH->new($hostname, user => $username, master_stderr_d
+iscard => 1}
$command = "cd /usr/local/bin; interactive_program.pl";
@out = $ssh->capture({stdin_data => "input1\ninput2\ninput3\n"}, $comm
+and);
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Though, I don't think that will solve your problem... the Expect approach seems more promising!