Here's a one liner (at least the real work is done in one line) that will get the job done. It ties all three files to arrays and then greps through them to find the common ones.

use strict;
use Tie::File;

tie my @f1, 'Tie::File', 'file1.txt' or die;
tie my @f2, 'Tie::File', 'file2.txt' or die;
tie my @f3, 'Tie::File', 'file3.txt' or die;

@f1 = grep { my $word = $_;
             my $size = $#f2;
             @f2 = grep { if ($_ eq $word) { push @f3, $_; 0 }
                          else { 1 } } @f2;
             $size == $#f2; } @f1;
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Outputs the following for your example files:

file1.txt

three
four
five
six
seven
[download]

file2.txt

nine
eleven
twenty
thirty
forty
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file3.txt

one
two
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