my @dirnames = qw(dir1 dir2 ...);

my %permissions = (
    user1 => {
        dir1 => 0,
        dir2 => 1,
        ...
    },
    user2 => {
        dir1 => 1,
        ...
    },
    ...
);

# Ein Element setzen:
$permissions{user1}{dir1} = 1; # usw.

# Alles auslesen und in CSV speichern:
open(my $csv, '>', 'CSV-FILE.csv') or die $!;
select $csv;
print ";$_" for @dirnames;
print "\n";

for my $user (keys %permissions) {
    print "$user;";
    for my $dir (@dirnames) {        
        print $permissions{$user}{$dir} ? "1;" : "0;";
    }
    print "\n";
}
select STDOUT;
close $csv;