A hierarchical model of heat transfer for the thermal analysis of electronic devices is presented. The integration of participating scales (from nanoscale to macroscales) is achieved by (i) estimating the input parameters and thermal properties to solve the Boltzmann transport equation (BTE) for phonons using molecular dynamics (MD), including phonon relaxation times, dispersion relations, group velocities, and specific heat, (ii) applying quantum corrections to the MD results to make them suitable for the solution of BTE, and (iii) numerically solving the BTE in space and time subject to different boundary and initial conditions. We apply our hierarchical model to estimate the silicon out-of-plane thermal conductivity and the thermal response of an silicon on insulator (SOI) device subject to Joule heating. We have found that relative phonon contribution to the overall conductivity changes as the dimension of the domain is reduced as a result of phonon confinement. The observed reduction in the thermal conductivity is produced by the progressive transition of modes in the diffusive regime (as in the bulk) to transitional and ballistic regimes as the film thickness is decreased. In addition, we have found that relaxation time expressions for optical phonons are important to describe the transient response of SOI devices and that the characteristic transport regimes, determined with Holland and Klemens phonon models, differ significantly.