Unmanned aircraft systems (UAS), or unmanned aerial vehicles (UAVs), often referred to as drones, have been experiencing healthy growth in the United States and around the world. The positive uses of UAS have the potential to save lives, increase safety and efficiency, and enable more effective science and engineering research. However, UAS are subject to threats stemming from increasing reliance on computer and communication technologies, which place public safety, national security, and individual privacy at risk. To promote safe, secure and privacy-respecting UAS operations, there is an urgent need for innovative technologies for detecting, tracking, identifying and mitigating UAS. A Counter-UAS (C-UAS) system is defined as a system or device capable of lawfully and safely disabling, disrupting, or seizing control of an unmanned aircraft or unmanned aircraft system. Over the past 5 years, significant research efforts have been made to detect, and mitigate UAS: detection technologies are based on acoustic, vision, passive radio frequency, radar, and data fusion; and mitigation technologies include physical capture or jamming. In this paper, we provide a comprehensive survey of existing literature in the area of C-UAS, identify the challenges in countering unauthorized or unsafe UAS, and evaluate the trends of detection and mitigation for protecting against UAS-based threats. The objective of this survey paper is to present a systematic introduction of C-UAS technologies, thus fostering a research community committed to the safe integration of UAS into the airspace system.