This paper describes UAV (Unmanned Aerial Vehicle) control system which employs PC104 modules. It is controlled by application program based on Linux OS. This application consists of both Linux device driver in kernel-space and user application in user-space. In order to get data required in the unmanned flight, external devices are connected to PC104 modules. We explain how Linux device drivers deal with data transmitted by external devices and we account for how the user application controls UAV on the basis of data processed in the device driver as well. Furthermore we look into the role of GCS (Ground Control Station) which is to monitor the state of UAV.