What is the form of the command? If it involves redirection, for example, perl does not directly execute the command but rather invokes the shell to do it. Thus, when you break out of the call, you are actually killing a shell invocation, not the offending process. While I hate to invoke bash-like magic, the simplest solution I have found involves actual process management and essentially grepping the results of ps. The following is code I use to handle this problem in one of my scripts: I invite criticism if someone has a better way. 
        my $pid = open my $calc, '-|', "$command 2>&1"
            or die "Pipe failed on open: $!\n";
        my $vector = '';
        vec($vector,fileno($calc),1) = 1; # Flip bit for pipe

        unless (select($vector,undef,undef,$timeout)) { # Calculation 
+is hanging
            # collect list of spawned processes
            my @pids = $pid;
            my $i = -1;
            push @pids, `ps --ppid $pids[$i] -o pid` =~ /\d+/g while +
++$i < @pids;
            kill 9, $_ for @pids;
            die "Calculation call failed to return with $timeout secon
+ds\n";
        }
        local $/; # Slurp
        my $content = <$calc>;
        close $calc;

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In reply to Re: Killing a system/exec/`` call if it times out by kennethk
in thread Killing a system/exec/`` call if it times out by Cagao

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