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An ad-hoc methodology for voxel-based geometry reconstruction is proposed. The reconstruction procedure outlined is fully automated and allows transforming explicit voxel RVE geometries into implicit smoothed geometries through a level set-based processing. During this post-processing, the yarns interpenetrations are suppressed, a thin gap is inserted between the contacting yarns and the fiber volume fraction is controlled locally by modifications of the yarns cross sections shapes. A conforming tetrahedral mesh can be subsequently generated based on the implicit geometrical description for finite elements simulations. Puck failure indices are used here to compare the damage initiation locations in the microstructure. Results show that damage initiates early and is rather randomly distributed in voxel-based discretizations, whereas it occurs more in the yarns contacting zones and in the higher fiber fraction volume regions for the smoothed RVE.