If parsing the HTML doesn't work then you could use regular expressions, something like this example:
$str = "aa<!--[if lt IE 7 ]><!--> <html lang=\"hi\" class=\"ie ie6\"> <!--<![endif]-->bb cc";
$pattern = "/(<!--[if\s[lg]+t\sIE\s[0-9]+\s]><!-->)(.*)(<!--<!\[endif\]-->)/";
$str = preg_replace($pattern, '', $str);
echo $str;
Or to keep the contents of the conditional tags:
$str = preg_replace($pattern, '$2', $str);
echo $str;