Time Domain Thermo-Reflectance (TDTR) experiments have been recently identified as a viable pathway toward extracting the phonon mean free path spectrum of semiconductor materials. However, this requires an intervening model. It is now widely believed that the frequency and polarization dependent phonon Boltzmann Transport Equation (BTE) is the most suitable model for this purpose. In this article, TDTR experiments are simulated using large-scale parallel computations of the phonon BTE in a two-dimensional computational domain. Silicon is used as the candidate substrate material. Simulations are performed for multiple pulse and modulation cycles of the TDTR pump laser. This requires resolution of a picosecond laser pulse within a computational timeframe that spans several hundreds of nanoseconds. The metallic transducer layer on top of the substrate is modeled using the Fourier law and coupled to the BTE within the silicon substrate. Studies are conducted for four different laser spot sizes and two different modulation frequencies. The BTE results are fitted to the Fourier law, and effective thermal conductivities are extracted. It is demonstrated that the time delay of the probe laser could have a significant impact on the fitted (extracted) thermal conductivity value. The modulation frequency is found to have negligible effect on the thermal conductivity, while the spot size variation exhibits significant impact. Both trends are found to be in agreement with experimental observations. The thermal conductivity accumulation function is also computed, and the effect of the mean free path spectrum on the thermal conductivity suppression is delineated. (C) 2016 Elsevier Ltd. All rights reserved.