I'd do the following:

1. For readability, make the foreach look something like:

   foreach my $filename (@file_list) {
       chomp $filename;
       clean_file($filename);
   }
   [download]

2. Don't use the indirect form of any method, especially a constructor. Tell Perl what you want instead of depending on Perl to do the right thing. It's better to be 100% safe instead of 99% safe. Instead, do:

       my $h = HTML::Clean->new($filename, 9);
   [download]

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