spool each email into an array using [man]explode[/man] (or [man]file[/man] if each email is a separate file) then do something like:
foreach ($array as $key => $value)
{
$value = trim($value);
if ($value{0} == '>') {unset($array[$key]);}
}
$cleaned_up_email = implode("\n", $array);
echo $cleaned_up_email;