Many modern applications of lasers involve understanding the transport of radiation through thin layers. The interactions of continuous wave and pulsed lasers with skin in dermatological use related to surgery and cosmetic procedures are examples of such. These highly scattering thin layers in skin are best modeled by the Monte Carlo method. However, most traditional Monte Carlo models may inaccurately account for the presence of thin layers. As an example, the very thin epidermis, with its highly absorbing melanin, is known to influence laser penetration significantly. If the Monte Carlo model is implemented without special features, then the results of the simulation will show incorrect effects of thin layers because the path length of most photons would be significantly larger than the layer thickness. As a result, the computed photon travel path length would simply not feel the presence of the layer. In this study, we present numerical and algorithmic features for computation of radiation transport through thin layers. It is noted that, while Monte Carlo without special features smears the radiative effect of the layers, the refined technique indicates that layers have a great impact on the absorption of energy, especially if the layer properties are distinctly different from those of the adjacent layers. The findings have significant implications in the study of diagnostic and therapeutic applications of lasers in biomedicine and surgery. The results show that absorbing layers have significant influence on the radiative transport in multilayers, even if they are very thin. Boundary effects arising from the optical property mismatch as well as the changes to photon path length distribution are more pronounced for thin layers since the ratio of surface area to volume is larger.