I guess you're working with Class::Struct.

You don't show enough code so I can't tell you directly what to do, but I was able to create an array of the structures and populate an array reference inside:

#!/usr/bin/perl
use warnings;
use strict;

use Class::Struct;
use Data::Dumper;

struct(Scale  => {
    name   => '$',
    offset => '$',
    foo    => '$',
    index  => '$',
    chords => '@',
    notes  => '@'
});

my @scales = map 'Scale'->new, 1 .. 5;
push @{ $scales[0]->chords }, 'Ami';

print Dumper \@scales;
[download]

Beginning of the output:

$VAR1 = [
          bless( {
                   'Scale::foo' => undef,
                   'Scale::chords' => [
                                 'Ami'
                               ],
                   'Scale::notes' => [],
                   'Scale::offset' => undef,
                   'Scale::name' => undef,
                   'Scale::index' => undef
                 }, 'Scale' ),
          bless( {
...
[download]

Update: Fixed the code example.