#! perl -w scipt
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Do you really want that shebang line?!?

use strict;
use warnings;
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Good! But then no need for -w.

my @files;
my @List_of_commands; 
my $line;
my $file;
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Not that bad, but in Perl one seldom really needs to predeclare a long list of variables; it's better to declare them as close as possible to where they're actually needed.

while (<*.sql>) {
  push (@files,$_);
}
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Huh?!? Why not

my @files=<*.sql>;
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foreach (@files) {
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So why not avoiding to use the intermediate variable @files and just do

for (<*.sql>) {  # I never use C<foreach> ;-)
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  $file = $_;
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So why not limiting $file to this this lexical scope? Also it would be better to

• either use $_ directly,
• use the common perlish syntactic sugar:

  for my $file (<*.sql>) {  # I still prefer C<for> orver C<foreach>!!
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  open (FILE, "<$file");
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Didn't mummy told you to

1. always check the return value of opens and (somewhat less importantly) also to
2. use lexical filehandles and
3. the 3-args form of open?

  while (<FILE>){

    my $line = $_;
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Ditto as above!!

    if $line not =~ (/INSERT INTO Message_pool)/{
      #Do nothing
    }
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Hmmm sounds Perl6-ish. No, let me see better... oh, it's just a misplaced parenthesis. No, let me see better... they're two misplaced parens. Seems we've found the problem.

Incidentally, if #Do nothing is just a placeholder, then fine. But if you think you want to keep it like that, which is not totally unprobable, taking into account your coding {style,experience} as of what I could see above, then just know that eliminating the whole if statement will do just fine.

All in all I recommend reading some introductory Perl tutorial before going on...

Update: I gave a more comprehensive peek into the rest of your script and I think that it could be rewritten much more simply e.g. along this way:

#!/usr/bin/perl
# UNTESTED!

use strict;
use warnings;

open my $out, '>', "outfile.txt" or
  die "Can't open output file: $!\n";
select $out;

@ARGV=<*.sql>;
while (<>) {
    next unless /^.{0,50}CREATE TABLE
                 \s
                 ([A-Z|a-z|_]{5,40})
                 \s
                 .{1,100}/x;
    print "if exists (select 1 from INFORMATION_SCHEMA.tables where ta
+ble_name = '$1') DROP TABLE '$1'\n";
}

__END__
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Please note that I tried to keep as close as possible to your logic, but if it were just this functionality that you need, than I just wouldn't open the output file myself and use shell redirection instead. If this is to evolve into something bigger, then plainly ignore this comment! If it is not, then I would leave to the user to specify input and output on the cmd line:

#!/usr/bin/perl -ln

use strict;
use warnings;

BEGIN {@ARGV=map glob, @ARGV} # You're under Win*, aren't you?

next unless /$whatever (\w+) $whatever/;
print "whatever: $1";

__END__
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