Small scale autonomous aircraft have many applications in defense, rescue services, civilian forces, surveillance and other areas. Our project provides the ground work for an autonomous flight control and Global Positioning System (GPS) based navigation system on a small scale helicopter. Real-time data is collected on the craft via ultrasonic sensors, an inertial measurement unit (IMU), a GPS receiver and a digital compass. These data are input to an onboard hardware control system implemented on a Field Programmable Gate Array (FPGA). The intended final product will be an autonomous helicopter that can receive GPS coordinates, take off, fly to specified destinations and land at a designated location. The control system is designed to be modular, so that additional sensors and functions can be added in the future within the bounds of payload and space limitations. Completed are multiple subsystems including parsing of sensor data on an FPGA, onboard printed circuit board (PCB) design and a running software prototype for stable hovering.