So it's hard to say from your limited code example, but you are probably running into a situation where system is blocking the Tk event loop. Tk (and all GUI's) run a thing called the event loop..... your new MainWindow; and MainLoop; statements are what start it. Once MainLoop gets called, a big loop starts running behind the scenes, doing everything you ask, on a schedule. When you put a while(1) loop in Tk, or a system call, it will hog the whole loop until it finishes (system returns).

So...... you want to avoid system calls, unless they are in a piped open or somehow forked off. Since you are writing the results to an output file ( not collecting the results internally), you can fork off the system call, and let Tk keep running it's loop. So instead of system, fork and exec. Like:

 if(fork() == 0){ 
       exec( "$executable $title" )
         }
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I am trying to create an input file from the GUI which is done by calling the OUTFILE filehandle. Then, I want to take this file and pass it to a .exe program which reads the title of the file and creates output files. This is where I call system() and try to output it to a specific directory. Before calling system, I had to specify the folder where the .exe file is if not, perl looks into the default directory and does nothing. I hope this helps. As for a better example, I wish I could give you one better but I'm having a hard time working it out.

Here is something else I came up with after reading the docs you wrote:

my $title = "something";
#title of the input file
my $executable = "C:/Users/Desktop/file.exe";
# the .exe file where the input needs to be passed
my $output = "C:/Users/Desktop";
# folder where the generated output files need to be located
my $outfile = "C:/Users/Desktop/$title.in";
#location of the input file
    open(OUTFILE,">$outfile") or die "Can't open output file $outfile\
+n";
    print OUTFILE @array;
    close OUTFILE;

    my $msg = $mw->messageBox(-icon => "info", -type => "OK",
                              -title => 'Save', -message => "File was 
+successfully saved.");


 my @args = ("start",$executable,$title);
for (@args) {
  # Apply smart-ish double quotes
  if (/ /) { $_ = qq{"$_"}; }
};
 chdir $output;
#this command isn't working on Tk
system(@args) == 0
  or warn "Couldn't launch '$title' : $!/$?/$^E";
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This also works fine in perl but not in Tk. I think the problem here is that it doesn't locate the $output directory. I know that you chdir does nothing if the directory is not set properly. Is there another way of specifying the directory?