I'm guessing you want to process each line and write it out (untested)

#!perl
use strict;
use warnings;
use HTML::Strip;

my $hs = HTML::Strip->new();

my $files_dir = 'C:\Dwimperl\Perl';
my $write_dir = 'G:\research\sec filings 10k and 10Q\data\filing docs\
+1993\Clean';

opendir (my $dir_handle, $files_dir);
while (my $filename = readdir($dir_handle)){
  
  next unless -f $files_dir.'/'.$filename;
  print "Procesing $filename\n";
  open my $fh_in, '<', $files_dir.'/'.$filename
      or die "failed to open '$filename' for read";
  
  open my $fh_out, '>', $write_dir.'/'.$filename
      or die "failed to open '$filename' for write";
   
  my $count=0;   
  while (my $line = <$fh_in>) { 
    my $clean_text = $hs->parse($line);
    print $fh_out "$clean_text\n";
    ++$count;
  }   
  $hs->eof;  
  print "$count lines read from $filename\n;"  
}
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