Just open all the files that need opening then iterate through the file e.g

use IO::File;

my %fhs = map {
  my $fh = IO::File->new($_, 'w') or die "ack [$_]: $!";
  $_ => $fh;
} @natures;

while(<FILE>) {
  for my $match (keys %fhs) {
    print {$fhs{$match}} $_
      if /$match/;
  }
}

close $_ for values %fhs;
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So that will only open the files once and iterate through the file once, which should do what you want.