If the program can run with a "live" version that can boot on itself with a CD or USB drive, yes you can (in fact in those cases, the program includes a small "micro" OS to boot from there). Otherwise you would need to install also an operating system into a second virtual machine.
Just remember that a virtual machine, regardless what program was used to create it, behaves just like a normal computer, and if the program runs without an operating system on a real computer, it will on a virtual machine.