Cyber-Physical Systems (CPS) utilize different devices to collect sensitive data, communicate with other systems, and monitor essential processes in critical infrastructure applications. However, in the ecosystem of CPS, unauthorized or spoofed devices may danger or compromise the performance and security of the critical infrastructure. The unauthorized and spoofed devices may include tampered pieces of software or hardware components that can negatively impact CPS operations or collect vital CPS metrics from the network. Such devices can be outsider or insider threats trying to impersonate other real CPS devices via spoofing their legitimate identifications to gain access to systems, steal information, or spread malware. Device fingerprinting techniques are promising approaches to identify unauthorized or illegitimate devices. However, current fingerprinting solutions are not suitable as they disrupt critical real-time operations in CPS due to the nature of their extensive data analysis or too much overhead on the devices' computational resources. To address these concerns, in this work, we propose STOP-AND- FRISK (S&F), a novel fingerprinting framework to identify CPS device classes and complement traditional security mechanisms in CPS. S&F is based on a secure challenge/response mechanism that analyzes the behavior of the CPS devices at both the hardware and OS/kernel levels. Specifically, the proposed novel mechanism combines system and function call tracing techniques, signal processing, and hardware performance analysis to create specific device-class signatures. Then, the signatures are correlated against known behavioral ground-truth to identify the device types. To test the efficacy of S&F extensively, we implemented a realistic testbed that included different classes of CPS devices with a variety of computing resources, architectures, and configurations. Our experimental results reveal an excellent rate on the CPS device-class identification. Finally, extensive performance analysis demonstrates that the use of S&F yields minimal overhead on the CPS devices' computing resources.