We present results of Niobium based SQUID magnetometers for which the weak-links are engineered by the local oxidation of thin films using an Atomic Force Microscope (AFM). Firstly, we show that this technique allows the creation of variable thickness bridges with 10 nm lateral resolution. Precise control of the weak-link milling is offered by the possibility to realtime monitor weak-link conductance. Such a process is shown to enhance the magnetic field modulation hence the sensitivity of the magnetometer. Secondly, AFM lithography is used to provide a precise alignment of NanoSQUID weak-links with respect to a ferromagnetic iron dot. The magnetization switching of the near-field coupled particle is studied as a junction of the applied magnetic field direction.