In this contribution we critically review heat and mass transfer issues in the Focused Electron Beam Chemical Vapor Deposition (FEB-CVD). In general, the transport of both the precursor molecules and the primary/secondary electrons facilitate nanostructure deposition. Depending on the operating pressure either continuous advection–diffusion mass conservation equation or the kinetic Boltzmann Transport Equation (BTE) describes the transport of precursor molecules to the substrate surface. At the surface, some of the precursor molecules are adsorbed, spatially re-distributed by surface diffusion, and, finally, a fraction of the adsorbed molecules become converted into a solid deposit. This occurs upon interaction with back-scattered primary electrons and secondary electrons, yielded by the substrate and deposit upon impingement of the high-energy primary electron beam. The interactions of the primary electrons with the substrate and nanoscale-confined deposit possibly induce significant localized heating. Such energy transfer process is complex, involves non-classical heat conduction, and may greatly influence the deposition process. The pertinent question is then what controls the FEB-CVD process, i.e., both time dependent growth of the nanostructure and its shape evolution? The answer to this question can be obtained via complimentary theoretical and experimental studies, discussed here with the main focus on transport phenomena underlying FEB-CVD.