A UHV instrument is presented for in situ fabrication of nanostructures and in situ investigation of their magnetoresistance. Nanostructures of diverse shape and size are created from thin films utilizing a focused ion beam. The magnetic nanostructures are contacted via a micromanipulator, which makes it possible to address the individual structures. The system is additionally equipped with a scanning electron microscope column, which is used for damage-free navigation and control of the structuring and contacting. First magnetoresistance measurements of structures carved into a Permalloy film demonstrate the high sensitivity and the flexibility of the new setup.