Nanoscale phonon transport within silicon structures subjected to internal heat generation was explored. A Monte Carlo simulation was used. The simulation procedures differed from the current existing methods in which phonons below a predefined "reference temperature" were not accounted to reduce memory storage and computational resources. Results indicated that the heat diffusion equation significantly underestimates temperature distribution at nanoscales in the presence of an external heat source. Discussions on temperature distribution inside silicon thin film when heated by a pulsed laser, an electron beam or due to near-field thermal radiation effects were also provided. (C) 2011 Elsevier Ltd. All rights reserved.