In addition to productivity and quality output, for many years, manufacturing systems were also designed with reliability and safety requirements in mind. In the recent decade or so, the approach seems not adequate anymore. The current manufacturing global operations ask for more stringent requirements than ever before, which include privacy and security of transactions, among others. Manufacturing control is not new, but the use of cloud environments to integrate distributed manufacturing facilities and entirely control the production processes across those facilities is an active research area denoted in terms such as: virtual factory, cloud manufacturing, Industry 4.0, Industrial Internet of Things (IIoT), and more recently, software-defined networking-based (SDN-based) manufacturing. In computer networking domain, SDN is known as a network architecture that decouples the network data and control mechanisms. SDN architecture assigns the entire data control to a logically centralized control plane that can be software-programmed based on specific application needs. From the security point of view, this translates in the fact that anyone with access to the computers that run the network control software could potentially get control over the entire network. This paper proposes an integrated modeling environment that addresses the virtual manufacturing system assurance through cybersecurity and resilience mechanisms for SDN applications. First, the paper proposes a SDN-based manufacturing testbed and a combined cybersecurity-resilience ontology to be used for the requirements capture of the virtual manufacturing network design stages. Then, the paper outlines the framework for SDN-based cybersecurity-resilience protection mechanisms for virtual manufacturing applications, and ends with the envisioned future research needed for implementing the proposed framework.