use Fcntl qw/:flock/;
#list of directories to look in
my @directoryList=('/dir/dir1','/dir2');
#for each dir
foreach my $dir (@directoryList){
   #open dir
   opendir(DIRHANDLE, "$dir ") or die "could't open dir $!";
   #create array of files present in dir
   my @files=  grep(!/^\./,readdir(DIRHANDLE));
   #for each file test open and test lock
   foreach my $file (@files){
      open FILE , "/$dir/$file" || die "Could not open";
      #if lock obtained do your job
      if (flock (FILE,LOCK_EX)){
         #do your job on $file
      }
   }
}
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Instead of a foreach loop you could use map to map your jobs onto each file.