Seems to me that you need a hash of lists -- something like this (untested):

my %elements;
foreach (@lines) {
    my ($key, @items);
    chomp;
    ($key, @items) = split(/,/, $_);
    push @{ $elements{$key} }, [ @items ];
}
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That'll get you a hash, keyed by HRD, BGN, OTI or what have you. To get at all of the third items of HDR, your code is something like this:

foreach my $row (@{ $elements{HRD} }) {
    print $row->[2], "\n";        # remember, offset by one
}
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This *is* untested, but even if it's buggy, it'll be remarkably similar to the actual tested code. (I have a bit of a headache right now, and you should really see perlref and perldsc for the real scoop.) No warranty today.