Additionally, why use ls?

opendir(my $dh, '.')
  or die("Unable to list directory: $!\n");

my @searchlist = readdir($dh);
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or

opendir(my $dh, '.')
  or die("Unable to list directory: $!\n");

while (defined(my $file = readdir($dh))) {
   ...
}
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Combined with sachmet's solution:

opendir(my $dh, '.')
  or die("Unable to list directory: $!\n");

my @patterns = map { qr/\Q$_\E/ } 
               grep { /^\.\.?$/ }
               readdir($dh);

open(my $fh_in, 'test.txt')
   or die("Unable to open input file test.txt: $!\n");

while (my $line = <$fh_in>) {
   chomp $line;
   foreach my $pattern (@patterns) {
      print("Match found\n") if $line =~ $pattern;
   }
}
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Combined with holli's solution:

opendir(my $dh, '.')
  or die("Unable to list directory: $!\n");

my %searchlist = map { $_ => 1 }
                 grep { /^\.\.?$/ }
                 readdir($dh);

open(my $fh_in, 'test.txt')
   or die("Unable to open input file test.txt: $!\n");

while (my $line = <$fh_in>) {
   chomp $line;
   print("Match found\n") if $searchlist{$line};
}
[download]

Update: Fixed copy & paste error map { qr/\Q$pattern\E/ } => map { qr/\Q$_\E/ }.