use strict;
use warnings;

use Data::Dumper;

my @columns_duplicates = (
  [qw[1 2 3 2 4 4]],
  [qw[a b c b d d]],
  [qw[x y z y u u]]
);

print Dumper \@columns_duplicates;

my @columns_unique = do {
  my %seen;

  my @rows = grep {
    my $row = $_;

    not $seen{
      join "\0", map {
        $_->[$row]
      } @columns_duplicates
    }++
  } $[ .. $#{$columns_duplicates[0]};

  map {
    [ @$_[@rows] ]
  } @columns_duplicates;
};

print Dumper \@columns_unique;