Nanoscale three-dimensional (3D) surface modifications, by scanning tunneling microscopy under ambient conditions, of La0.7Sr0.3MnO3 thin films have been performed. It was demonstrated that there are well-defined combinations of bias voltages, tunneling current, and scan speeds which allow for controlled surface structuring. Lateral structures with sizes down to 1.5 nm are possible to obtain. Moreover, it is possible to reproducibly control the depth of etching with half a unit cell precision, enabling design of 3D surface structures and control of the surface termination of La0.7Sr0.3MnO3 through etching.