ww++. This is the only reasonable answer ... until you know what the data structure is, all the other solutions are just throwing code at the wall to see what sticks.

From the OP:

I can access each element by using @Data[$_]{ID}, @Data[$_]{Score}...

I assume this was a misprint for $Data[$_]{ID}, $Data[$_], since you are accessing single elements, not array slices.

it's array of array of hashes and chorobas code works.

Here is how choroba’s code works for me:

use strict;
use warnings;

my @data =
(
    { ID => 'AA', Score => 20 },
    { ID => 'D',  Score => 30 },
    { ID => 'F',  Score =>  7 },
    { ID => 'AA', Score =>  3 },
);

## choroba's solution:

my %by_id;
push @{ $by_id{ $_->{ID} } }, $_->{Score} for @data;

# Sort the scores for each id.
$_ = [ sort { $b <=> $a } @$_ ] for values %by_id;

# Sort the ids by the highest score.
for my $id (sort { $by_id{$b}[0] <=> $by_id{$a}[0] } keys %by_id) {
    print "ID: $id\tScore: $_\n" for @{ $by_id{$id} };
}
[download]

As you can see, there is only one array; i.e., @data is an array of hashes (AoH).

Hope that helps,

Athanasius <°(((>< contra mundum

Iustus alius egestas vitae, eros Piratica,