Treatment outcomes in radiotherapy can be improved by reducing uncertainties in patient set-up, beam delivery and dose distribution. Clarification of arrangements can minimize the dose distributed to normal tissues, and facilitate dose escalation. However, heterogeneity can increase any ambiguities associated with dose distribution. The treatment planning system (TPS) cannot effectively calculate dose distribution in complex heterogeneous areas, which increases uncertainty. This research aims to study microscopic dose distribution in temporal bone, cochlea and pancreatic stents as applicable to modern radiotherapy treatments. To achieve this aim a multiscale approach will be used, as it provides essential information about differences in dose distribution between TPS/clinical CT and Monte Carlo (MC)/Micro CT for photons and protons.In the first part of this study, two DICOM series of pancreatic cancer patients were used with an inserted stent. A new model includes the atomic composition of the stent material, and new stent contouring was introduced to overcome a CT artefact. A PRIMO Monte Carlo model was tuned and compared with the TPS dose distribution and a one-beam volume-modulated arc therapy (VMAT) plan was created. A significant dose difference was observed when comparing the new model and TPS, suggesting increased uncertainty of the dose distribution in clinical practice.An open-access DICOM format of the data for the resected temporal bone and cochlea tissue was used with the FLUKA MC code to imitate potential high-dose scenarios associated with VMAT using the FLOOD option. Twenty-three photon and proton energy levels ranging from 0.055 to 5.5 MeV for photons and 37.59 to 124.83 MeV for protons were simulated separately to calculate dose distribution. Micro CT data shows three density levels in the temporal bone and cochlea. The photon distribution in the low energy range 0.055-0.09 MeV, the largest proportion of the dose (48.8%) was deposited within high-density bone, whereas above 0.125 MeV, the change on dose distribution started to occur where there was greater deposition in low-density tissue, reaching 53%. The dose distribution in the soft bone's intermediate density was 26.4% at 0.07 MeV and dropped to 19.7% at 2.5 MeV. There is a 29% percentage difference in dose distribution on the soft bone between the low and high energy. The dose distribution did not change significantly in proton between the low, intermediate and high-density areas. The dose distribution in 37.59 MeV shows 54.86% in low density, 19.75% in intermediate density and 25.39% in high density. A similar outcome was observed in high energy 124.83 MeV, a dose distribution was 54.21% in low density, 19.79% intermediate density and 26% in high density.An advanced model was created to connect the results to a clinical routine when treating brain tumours using the VMAT technique. Cases were selected from 280 data sets of patients diagnosis with gliomas. Eleven different scenarios were identified. The advanced model shows five cases with a...