There is nothing wrong in using Text::CSV_XS so far. The problem is how to restructure the information. You can use the following code as an inspiration:

#!/usr/bin/perl

use warnings;
use strict;
use feature 'say';

use Text::CSV_XS;

use Data::Dumper;

my $csv = Text::CSV_XS->new();

$_ = <DATA>;
$csv->parse($_);
my @companies = $csv->fields;
splice @companies, 0, 2;

my %hash;
while (<DATA>) {
    $csv->parse($_);
    my @fields = $csv->fields;
    for my $i (0 .. $#companies) {
        $hash{$companies[$i]}{$fields[1]} = $fields[2 + $i];
    }
}

print Dumper \%hash;

__DATA__
Product Name,Product Code,Company1,Company2,Company3
Test One,C001,Y,N,N
Test Two,C002,N,N,Y
Test Three,C003,Y,Y,N
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