Your script will store the contents of the file in memory twice.
This one will create the necessary arrays and fill them directly while reading the file.

#!/usr/bin/perl -w
use strict;

# create three empty array references
my %arrays = map {$_, []} qw ( A B C );

my $ar_ref = undef;

while (<DATA>) {
    if (/ABC header line (\w)/) {
        die "unrecognized header <$1>\n" unless exists $arrays{$1};
        $ar_ref = $arrays{$1};
    }
    else {
        die "no current array\n" unless $ar_ref;
        chomp;
        push @$ar_ref, $_;
    }
}

for (keys %arrays) {
    print "$_ => ( @{$arrays{$_}} )\n";
}

__DATA__
ABC header line A
A line 1
A line 2
A line 3
A line 4
ABC header line B
B line 1
B line 2
B line 3
ABC header line C
C line 1
C line 2
C line 3
C line 4
[download]

And this is the result:

A => ( A line 1 A line 2 A line 3 A line 4 )
B => ( B line 1 B line 2 B line 3 )
C => ( C line 1 C line 2 C line 3 C line 4 )
[download]

HTH

cchampion