Techniques are described for separating control plane functions in a network device using virtual machines. The techniques include initializing multiple virtual machine instances in a control unit of a standalone router, and running different control processes for the router in each of the virtual machines. For example, in a root system domain (RSD)-protected system domain (PSD) system, a control unit of the standalone router may support a RSD virtual machine (VM) and one or more PSD VMs configured to form logical devices and execute logically separate control processes without requiring physically separate, hardware-independent routing engines to form the PSDs. Each of the RSD VM and PSD VMs includes a separate kernel, an operating system, and control processes for the logical device. When a software failure occurs in the PSD VM, the PSD VM may perform a software failover without affecting the operation of the RSD VM.