Uninhabited vehicles can be used in many applications and domains, particularly in environments that humans cannot enter (e.g. deep sea) or prefer not to enter (e.g. war zones). The promise of relatively low cost, highly reliable and effective assets that are not subject to the physical, psychological or training constraints of human pilots has led to much research effort across the world. Due to technological advances and increasing investment, interest in Unmanned Aerial Vehicles (UAVs) as a practical, deployable technological component in many civil applications is rapidly increasing and becoming a reality, as are their capabilities and availability. UAV platforms also offer a unique experimental environment for developing, integrating and experimenting with many other technologies such as automated planners, knowledge representation systems, chronicle recognition systems, etc. UAV performs various kinds of missions such as mobile tactical reconnaissance, surveillance, law enforcement, search and rescue, land management, environmental monitoring, disaster management. UAV is a complex and challenging system to develop. It operates autonomously in unknown and dynamically changing environment. This requires different types of subsystems to cooperate. In order to realize all functionalities of the UAV, the software part becomes very complex real-time system expected to execute real-time tasks concurrently. This paper describes proposed software architecture for GCS (Ground Control Station) for lightweight UAV purpose-built for medium-scale reconnaissance and surveillance missions in civil area. The overall system architecture and implementation are described.