Unmanned Aerial Vehicles (UAVs) have recently rapidly grown to facilitate a wide range of innovative applications that can fundamentally change the way cyber-physical systems (CPSs) are designed. CPSs are a modern generation of systems with synergic cooperation between computational and physical potentials that can interact with humans through several new mechanisms. The main advantages of using UAVs in CPS application is their exceptional features, including their mobility, dynamism, effortless deployment, adaptive altitude, agility, adjustability, and effective appraisal of real-world functions anytime and anywhere. Furthermore, from the technology perspective, UAVs are predicted to be a vital element of the development of advanced CPSs. Therefore, in this survey, we aim to pinpoint the most fundamental and important design challenges of multi-UAV systems for CPS applications. We highlight key and versatile aspects that span the coverage and tracking of targets and infrastructure objects, energy-efficient navigation, and image analysis using machine learning for fine-grained CPS applications. Key prototypes and testbeds are also investigated to show how these practical technologies can facilitate CPS applications. We present and propose state-of-the-art algorithms to address design challenges with both quantitative and qualitative methods and map these challenges with important CPS applications to draw insightful conclusions on the challenges of each application. Finally, we summarize potential new directions and ideas that could shape future research in these areas.