If your target OS is one with a native fork then that or one of the CPAN wrappers is possibly the way to go, but if you wanted a threads solution, your attempt was making a mountain out of a molehill.

There is certainly no logic to using 3 queues to pass the path, the filename, and the path+filename. Pass it once and split it up there if need be.

And there is no need to count the threads or detect when one has finished. Just start the number your want to use (say 4), and have them loop over the queue. As soon as they finish one piece of work they'll pick up the next automatically. It is also far more efficient than starting a new thread for each file.

When you've finished pushing all the filenames, push 4 undefs and the threads will self terminate when there is nothing left to do. Simplicity itself.

#! perl -slw
use strict;
use threads;
use Thread::Queue;
use File::Find;
use File::Copy;
use File::Path;

my $THREADS = 4;

my $Q = new Thread::Queue;

sub worker {
    while( my $path = $Q->dequeue ) {
        print "Creating directory" . $workdirectory . "\n";
        mkpath($workdirectory);
        copyfiles(
            $workdirectory, 
            $FilenamewithpathQueue->dequeue, $filename[0]
        );

        print "Processing Calculations...\n";
        open(RUNSCRIPT,">runscript.bash");

        print RUNSCRIPT <<EOD
        cd $workdirectory
        perl scriptthatincludesfortran.pl >& $workbasedirectory/$filen
+ame[0].log
EOD

        close(RUNSCRIPT);
        if (system("bash runscript.bash") != 0) {
            die "failed!\n";}
        else {
            print "done!\n";
        }

        print "bash $workdirectory/runscript.bash\n";
        print "\n";

    }
}

my @threads = map{ threads->create( \&worker ) } 1 .. $THREADS;

find( sub{ $Q->enqueue( $File::Find::name ) }, $basedirectory );

$Q->enqueue( (undef) x $THREADS );
$_->join for @threads;
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The code is untested because I couldn't make much sense of your OP code, as half the variables in it are never declared and never initialised.