my $dir = '/some/directory/here';
my @files = <$dir/\d{6}*>;     # All the relevant files start with 6 numbers, so don't glob others!

foreach (@files) {
      $inputfile = $_;
      [open $inputfile for reading, this code works fine]
      ....
      $outputfile = $inputfile;
      open NEWFILE, '>', "$dir/subdirectory/$outputfile" | die "Can't open $dir/subdirectory/$outputfile for writing: $!";
      .....
}