A separate timer thread will work if you set it up right, I don't understand why it wouldn't. You start 2 threads, which run independent. When the timer reaches the end of it's code block, if a finished flag isn't set, it kills the pid from the other thread. But I don't use windows, and maybe I don't experience it's peculiarities. This works on linux. (Granted it is easier if you have an eventloop system in main).

#!/usr/bin/perl -w
use strict;
use threads;
use threads::shared;

#my $finished:shared = 0;
my $timer_go:shared = 0;
#my $worker_go:shared = 0;
#my $worker_pid:shared = '';

my $worker = threads->create(\&worker);
my $timer = threads->create(\&timer,$worker);


print "hit enter to start\n";
<>;
$timer_go=1;
<>;

$timer->join();
$worker->join();


sub timer {
  my $worker = shift;
   while(1){     
       if($timer_go){
        my $count = 0;
             while(1){ 
                  $count++;
                  if($count > 5){    
                         print "timed out\nHit enter to finish\n";
                          # Send a signal to a thread
                         $worker->kill('INT');
                         return;
                        } 
                  sleep 1;
                  print "timing $count\n";
            }
       }else{sleep 1}
    }
}

sub worker {
       $|++;
       $SIG{INT} = sub{ warn "Caught Zap!\n"; sleep 1; exit; };
       my $worker_pid = open( READ, "top -d 1 -b |" );
       print "\t$worker_pid\n";
       return;
}
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