The UAV (Unmanned Aerial Vehicle) systems like unmanned autonomous helicopters are used in various missions of flight navigation and used to collect the environmental information of the surroundings. To realize the full functionalities of the UAV, the software part becomes a challenging problem. In this paper embedded real-time software architecture for unmanned autonomous helicopter is proposed that guarantee real-time performance of hard-real time tasks and re-configurability of soft-real time and non-real time tasks. The proposed software architecture has four layers: hardware, execution, service agent and remote user interface layer according to the reactiveness level for external events. In addition, the layered separation of concurrent tasks makes different kinds of mission reconfiguration possible in the system. An Unmanned autonomous helicopter system was implemented (Kyosho RC Helicopter) in our lab to test and evaluate the performance of the proposed system.