use strict;
use warnings;

my $content = do{local $/; <DATA>};

$content =~ s/(<surname>(?:(?:(?!<\/surname>).)*)<\/surname>\,?\s*<givenname>(?:(?:(?!<\/givenname>).)*)<\/givenname>)/<au>$1<\/au>/gsi;
$content =~ s/(<\/givenname>\,\s*)<au>(\s*<surname>)/$1$2/gis;
$content =~ s/(<\/givenname>\s*)<\/au>(\,\s*<surname>)/$1$2/gis;
$content =~ s/(<givenname>(?:(?:(?!<\/givenname>).)*)<\/givenname>\,?\s*<surname>(?:(?:(?!<\/surname>).)*)<\/surname>)/<au>$1<\/au>/gsi;

print $content;

__DATA__
<surname>Coff</surname>, <givenname>D.,</givenname> et al., <givenname>J.</givenname> <surname>Amat</surname> <surname>Coffman</surname>, <givenname>D.D.,</givenname>
<givenname>D.,</givenname>, <surname>Coff</surname> et al., <givenname>J.</givenname> <surname>Amat</surname> <surname>Coffman</surname>, <givenname>D.D.,</givenname>

output:
-------
<au><surname>Coff</surname>, <givenname>D.,</givenname></au>, <au><surname>Coff</surname>, <givenname>D.,</givenname></au> 
<au><givenname>D.,</givenname>, <surname>Coff</surname></au>, <au><givenname>D.,</givenname>, <surname>Coff</surname></au>