The aim of this paper is the modelling of urban microclimate, based on the limits imposed by the complexity of the three-dimensional space of cities. To this purpose, different Bioclimatic Scenarios were investigated through the microclimatic simulations using the micro-scale numerical model, ENVI-met 4v, applied in a case study of a Block in a highly residential neighbourhood of Athens. The study compares the bioclimatic scenarios of the roof top and road side vegetation plan in the current conditions, in order to evaluate how the existence of vegetation can affect the local air temperature and the thermal comfort condition of urban environment. This study also highlights the need to manage those microclimate data, through a geodatabase and provides a GIS approach of data organization and visualization. Creating building facades of the distributed temperature has showed that urban morphology parameters have an obvious impact on temperature distribution in the 3D space. On the other hand, the proposed roadside vegetation scenario has proved to be the most suitable way to improve the thermal comfort conditions of urban environment, as it can eliminate the Urban Heat Island (UHI) effects.