The objective of this thesis is to introduce innovative side-channel analysis methods, tools, and techniques with the capabilities to characterize and defend against the growing threat of malicious hardware alterations made to integrated circuitry and cyber-physical systems. Validating the authenticity and security of an electronic device has never been more important in the modern era. A global manufacturing supply chain and the increasing prevalence of network-connected electronics in everyday life is cause for concern. Existing software-based security techniques are insufficient to protect against alterations made to hardware at the silicon level, and detection of such alterations is traditionally a time-intensive, destructive, and often fruitless effort. Through unintended sources of information leakage such as the electromagnetic, acoustic, thermal, power, and timing side-channels, researchers have demonstrated a number of non-destructive hardware characterization and validation schemes. This research attempts to further those efforts by developing tools and techniques designed to improve the collection, analysis, monitoring, and ultimately, attack detection, based on circuit activity harmonics of the EM backscattering side-channel.