The characterization of advanced materials and devices in the nanometer range requires complex tools, and the data analysis at the atomic level is required to understand the precise links between structure and properties. This paper demonstrates that the atomic-scale modelling of graphene-based defects may be performed efficiently for various structural arrangements using the Brenner module of the SAMSON software platform. The signatures of all kinds of defects are computed in terms of energy and scanning transmission electron microscopy simulated images. The results are in good agreement with all theoretical and experimental data available. This original methodology is an excellent compromise between the speed and the precision required by the semiconductor industry and opens the possibility of realistic in-silico research conjugated to experimental nanocharacterisation of these promising materials. Copyright © 2018 by SCITEPRESS-Science and Technology Publications, Lda. All rights reserved.