my @in = grep { /\.txt$/ } readdir IN; # read all file names form dir 
+except names started with dot
[download]

Your code does not exclude file names that start with a dot (hidden files). To do that you need this:

my @in = grep { !/^\./ && /\.txt$/ } readdir IN; # read all file names
+ from dir except names started with dot
[download]

  open IN, '<', "Outpatient/$in" || next;
  open OUT, '>', "TXT/$in" || die "can't open file Formatted/$in";
[download]

Your opens will not fail correctly because of the high precedence of the || operator.

You need to either use the or operator (low precedence):

  open IN, '<', "Outpatient/$in" or next;
  open OUT, '>', "TXT/$in" or die "can't open file Formatted/$in";
[download]

Or use parentheses:

  open( IN, '<', "Outpatient/$in" ) || next;
  open( OUT, '>', "TXT/$in" ) || die "can't open file Formatted/$in";
[download]

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