Whereas the application of optically or magnetically heated nanoparticles to destroy tumours is now well established, the extension of this concept to target pathogens has barely begun. Here we examine the challenge of targeting pathogens by this means and, in particular, explore the issues of power density and heat transfer. Depending on the rate of heating, either hyperthermia or thermoablation may occur. This division of the field is fundamental and implies very different sources of excitation and heat transfer for the two modes, and different strategies for their clinical application. Heating by isolated nanoparticles and by agglomerates of nanoparticles is compared: hyperthermia is much more readily achieved with agglomerates and for large target volumes, a factor which favours magnetic excitation and moderate power densities. In contrast, destruction of planktonic pathogens is best achieved by localised thermoablation and very high power density, a scenario that is best delivered by pulsed optical excitation.