I think what you're wanting is to put the values you're getting into an array that can be seen thoughout the scope of the while and after it:

my @myfile_numbers = ();

while (my $pointer = $sth->fetchrow_hashref){
  $c++;
  $myfile_number = &cleaner ($pointer->{'file#'});
  push @myfile_numbers, $myfile_number;
}
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Now you'd have the array @myfile_numbers available after the loop has completed containing the values you read in the order you read them.