>Is there a way to spawn the system call in a separate thread or some other means such that I'm not hanging the program waiting for the user to close the viewing exe?

Say

my $File = "perl script.pl &"
my $returnValue = system($File);
print "Done.  ReturnValue $returnValue\r\n";

#rest of the program goes here
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Please note the ampersand (&) in the system call.
Here, the system will not be waiting for the execution of the script specified in the $File variable. It just proceeds with the next line and the system call will be running in the background.
Is this what you need?