Change it to this and am now getting the list but it has not removed the duplicates. Still lost

 #!/usr/bin/perl

use warnings;
use strict;

my $upload = "/var/tmp/work/upload";
my $work = "/var/tmp/work/STAP-domain_clean_project";
my $input3 = "$upload/domain.csv";

system ("dos2unix $input3");

open (IN,"$input3");
open (OUT,">>$work/local.rules");
while (<IN>) {
        chomp();

        if ($_ =~ /^.+\.([A-Za-z0-9-_]+\.[A-Za-z]{2,})$/){
        my @array = $1;
        my %seen = ();
        my @unique = grep { ! $seen{ @array }++ } @array;
                print "@unique\n";
        }
}
[download]

Your code redefines %seen and @array each time you read a line from your file. You get duplicates because your hash is always empty when you test it for a value.

The following will produce a list of the unique values from IN:

my (%seen,@unique);
while (<IN>) {
  chomp;
  $seen{$1}++ if ($_ =~ /^.+\.([A-Za-z0-9-_]+\.[A-Za-z]{2,})$/);
}
@unique = keys %seen;
printf "%s, ",$_ for @unique;
print "\n";
[download]

Updated for readability and coherence and typos (is it Monday already?)

1 Peter 4:10

Thank you! I understand now

... now getting the list but it has not removed the duplicates.
...
    my @array = $1;


On every iteration through the while-loop, this statement creates a new array and initializes it with a single element: the string that was captured to $1. This string is, of course, unique!