One problem is that you need to change the separator character for Text::CSV to ";". Another problem is that you are not populating your HASHES OF HASHES data structure. I created 2 tiny CSV files for myself, named 1.csv and 2.csv.

use strict;
use warnings;
use Data::Dumper;
use Text::CSV;
use File::Basename;

my @files = glob '*.csv';

my %hMFD;
foreach my $file (@files){
        my $file_base = fileparse($file, qr/\.csv/);
        my $csv = Text::CSV->new({sep_char => ';'});
        open (CSV, "<", $file) or die $!;
        while (<CSV>) {
                if ($csv->parse($_)) {
                    my @columns = $csv->fields();
                    $hMFD{$file_base}{$columns[0]} = $columns[1];
                }
                else {
                    my $err = $csv->error_input;
                    print "Failed to parse line: $err";
                }
        }
        close CSV;
}

print Dumper(\%hMFD);

__END__

$VAR1 = {
          '1' => {
                   'Table' => 'M',
                   'Data' => 'O'
                 },
          '2' => {
                   'Table' => 'X',
                   'Data' => 'Y'
                 }
        };
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