use Parallel::ForkManager;
my $pm = new Parallel::ForkManager($MAX_PROCESSES);

# ...

foreach my $f (@files) {
  if ( (-d $f) and ($f ne ".") and ($f ne "..") ){
     my $pid = $pm->start and next;
     chdir ...
     system ...
     system ...
     system ...
     $pm->finish;
  }
}
$pm->wait_all_children;