Additive manufacturing (AM) is one the fastest-growing industrial fields in the past decade. Initially used for prototyping of parts, additive manufacturing was also referred to as rapid prototyping. Advancement in technologies has now changed this field into a mainstream production method. One of the main advantages of additive manufacturing is that the entire process chain can be completely digital, where a product is designed in computer-aided design (CAD) software and then the processed files are sent via the Internet to a 3D printer to print the object anywhere around the world. The digital nature of the additive manufacturing cyber-physical system makes it vulnerable to cybersecurity risks such as sabotage and intellectual property theft. A novel design methodology is presented in this chapter that describes the possibility of embedding design elements in CAD files as security features. In the presence of these features, the CAD files print as high-quality components only under a specific set of process flow conditions. Any other processing parameters result in embedded defects that reduce the product quality and make it possible to identify counterfeit products. Such security features can augment the network security tools deployed by cybersecurity experts in the additive manufacturing process chain and provide an additional layer of security.