my (@output, @output1);
for my $i (0 .. $#array) {
    if (exists $hash{ $array[$i] }
            and $array1[$i] == $hash{ $array[$i] }{highest}) {
        push @output,  $array[$i];
        push @output1, $array1[$i];
    }
    else {
        push @output,  '';  # or use spaces ' ' here 
        push @output1, '';  # or whatever you want
    }

}