Nanotechnology remains one of the most active and intriguing research and development areas. While the importance of novel devices and systems engineered at the nanoscale is steadily increasing, the success of future nanoscale applications will depend on the effective implementation of nanomachining and nanomanufacturing platforms. This book addresses the significant role played by thermal transport in electron-beam based processes, considering the various time and length scales relevant from the macroscale to the nanoscale levels. In particular, it reviews and highlights thermal transport theories related to "nanomachining," a term loosely defined as the ability to shape, form, or build new structures at the nanoscale (1--100 nm). Beginning with an overview of nanomachining, the monograph introduces the relevant particle models based on the Boltzmann transport equation. Following general concepts, specific details for the electron-beam transport equation, radiative transfer equation, and phonon radiative transport equation are introduced. Attention is then paid to modelling of thermal transport at the nanoscale, including electron-beam propagation, the electronic thermal conduction, and the phonon transport, using various Monte Carlo methods. Simulations of different processes relevant to nanomachining are described in detail, including those for the two-temperature model and the electron-phonon hydrodynamics model. Also, parallelization strategies for the solution of the governing equations are outlined and both the hardware and software requirements are summarized. Finally the concept of molecular dynamics is introduced and its fundamentals are presented for understanding of nanomachining at the molecular level.