Focused electron beam induced deposition and etching (FEBID and FEBIE) are direct-write nanofabrication techniques in which an electron beam is used to achieve nanostructure functionalization, etching or deposition. Either alone or in combination with in situ plasmas, these techniques can also be used to accelerate reactions that occur in ambient environment, with simultaneous high-resolution imaging. Here, we describe our recent work on etching, functionalization and directed assembly of a range of nano- and two-dimensional materials using temperature-dependent FEBIE experiments in an environmental scanning electron microscope (ESEM). As examples of the application of these techniques, we demonstrate processes for assembling arrays of nanodiamonds that can be used as magnetic field sensors, as well as for controlled etching of hexagonal boron nitride (hBN) and black phosphorus (BP).