in reply to Improvement suggestions?

I'd do the following:
  1. For readability, make the foreach look something like:
    foreach my $filename (@file_list) { chomp $filename; clean_file($filename); }
  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);

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