Normalise the key (remove the junk characters) and use it as a hash key. 
my %seen;
while (<>) {
   my @fields = ...;
   my $key = normalise($fields[0]);
   print { $seen{$key}++ ? $unique_fh : $extras_fh } $_;
}

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In reply to Re: Remove duplicate entries by ikegami
in thread Remove duplicate entries by PyrexKidd

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