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Thanks to ground-based infrared and sub-mm observations the study of the dusty torus of nearby AGN has greatly advanced in the last years. With the aim of further investigating the nuclear mid-infrared emission of the archetypal Seyfert 2 galaxy NGC1068, here we present a fitting to the N- and Q-band Michelle/Gemini spectra. We initially test several available SED libraries, including a smooth, clumpy and two phase torus models, and a clumpy disk plus wind model. Although, the smooth torus model describe the spectra of NGC1068 if we allow to vary some model parameters among the two spectral bands. Motivated by this result, we produced new SEDs using the radiative transfer code SKIRT. We use two concentric tori that allow us to test a more complex geometry. We test different values for the inner and outer radii, half opening angle, radial and polar exponent of the power-law density profile, opacity, and viewing angle. Furthermore, we also test the dust grains size and different optical and calorimetric properties of silicate grains. The best fitting model consists of two concentric components with outer radii of 1.8 and 28 pc, respectively. We find that the size and the optical and calorimetric properties of graphite and silicate grains in the dust structure are key to reproduce the spectra of NGC1068. We conclude that the dust in NGC1068 reaches different scales, where the highest contribution to the mid-infrared is given by a central and compact component. A less dense and extended component is present, which can be either part of the same torus (conforming a flared disk) or can represent the emission of a polar dust component, as already suggested from interferometric observations.