We explore physically self-consistent models of dusty molecular tori in Active Galactic Nuclei (AGN) with the goal of interpreting VLTI observations and fitting high resolution mid-IR spectral energy distributions (SEDs). The input dust distribution is analytically calculated by assuming hydrostatic equilibrium between pressure forces - due to the turbulent motion of the gas clouds - and gravitational and centrifugal forces as a result of the contribution of the nuclear stellar distribution and the central black hole. For a fully three-dimensional treatment of the radiative transfer problem through the tori we employ the Monte Carlo code MC3D. We find that in homogeneous dust distributions the observed mid-infrared emission is dominated by the inner funnel of the torus, even when observing along the equatorial plane. Therefore, the stratification of the distribution of dust grains - both in terms of size and composition - cannot be neglected. In the current study we only include the effect of different sublimation radii which significantly alters the SED in comparison to models that assume an average dust grain property with a common sublimation radius, and suppresses the silicate emission feature at 9.7 micron. In this way we are able to fit the mean SED of both type I and type II AGN very well. Our fit of special objects for which high angular resolution observations (less than 0.3 arcseconds) are available indicates that the hottest dust in NGC 1068 reaches the sublimation temperature while the maximum dust temperature in the low-luminosity AGN Circinus falls short of 1000 K.