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

use Text::CSV_XS;

my $csv = Text::CSV_XS->new({ binary => 1, allow_whitespace => 1, }) 
  or die "Cannot use CSV: " . Text::CSV_XS->error_diag();

# for testing; in real world, open file and use that handle
my $fh = \*DATA;

my (%hash, @hdr);

while ( my $row = $csv->getline( $fh ) ) { 

    # header not yet defined? or 1st cell starts with '<' ==> use row as header
    if ( !@hdr || $row->[0] =~ m/^</ ) {
        @hdr = @{$row};
        next;
    }
    # otherwise try to process data
    else {
        for my $i ( 0 .. $#hdr ) {
            # only add those values which contain at least one character
            # so: no "undef"s or empty strings in result
            # if empty strings are OK or wanted, try to replace length() with defined()
            push @{ $hash{$hdr[$i]} }, ( length $row->[$i] ? $row->[$i] : () );
        }
    }
}

# check created data structure
require Data::Dumper;
$Data::Dumper::Sortkeys = 1;
print Data::Dumper::Dumper( \%hash );

__DATA__
<A1>,   <A2>,   <A3>
a1,     aa1,    aaa1
a2,	    ,    aaa2
a3,     aa3
a4

<B1>,   <B2>
b1,     bb1
b2,     bb2
b3

##</code><code>##

$VAR1 = {
          '<A1>' => [
                      'a1',
                      'a2',
                      'a3',
                      'a4'
                    ],
          '<A2>' => [
                      'aa1',
                      'aa3'
                    ],
          '<A3>' => [
                      'aaa1',
                      'aaa2'
                    ],
          '<B1>' => [
                      'b1',
                      'b2',
                      'b3'
                    ],
          '<B2>' => [
                      'bb1',
                      'bb2'
                    ]
        };