my %seen_values;
for my $aref (@array_of_arrayrefs) {
  $aref = [ map { $seen_values{$_}++ ? () : $_ } @$aref ];
}

##</code><code>##

my %seen_values;
my @new_AofA = map { $seen_values{$_->[0]}{$_->[1]}++ ? () : $_ } @AofA;