if(($array1[0]=~/c/i) && ($array2[0]= ~/c/i)) { if ($arra1[2]=array2[2] && array1[4]=array2[4]) { don't add anything } else { append matched line to file2 } } elsif(($array1[0]=~/M/i) && ($array2[0]= ~/M/i)) { if ($arra1[2]=array2[2] && array1[4]=array2[4]) { don't add anything } else { append matched line to file2 } }