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