Airborne magnetic data are commonly processed and interpreted to produce preliminary geological maps. Machine learning has the potential to partly fulfill this task rapidly and objectively, as geological mapping is comparable to a semantic segmentation problem that can be solved with a convolutional neural network. Because this method requires a high-quality dataset, we developed a data augmentation workflow that uses a 3D geological and petrophysical (magnetic susceptibility) model as input. The workflow uses soft-constrained Multi-Point Statistics, to create many synthetic 3D geological models, and Sequential Gaussian Simulation algorithms, to populate the models with the appropriate magnetic distribution. Then, forward modeling is used to compute the airborne magnetic responses of the synthetic models, which are associated with their counterpart surficial lithologies. We applied this workflow on a 3D model of the geology and magnetic susceptibility of the Malartic Mine area to obtain a large airborne magnetic synthetic dataset, associated with surficial lithologies, and perform segmentation. A Gated Shape Convolutional Neural Network algorithm was trained on this synthetic dataset to perform geological mapping of the synthetic airborne magnetic data and detect lithological contacts. The algorithm also provides attention maps highlighting the structures at different scales, and clustering was applied to its high-level features to do a semi-supervised segmentation of the area. The validation conducted on a portion of the synthetic dataset shows that the methodology is suitable to segment the surficial geology using airborne magnetic data. We also used transfer learning to test the trained model on measured magnetic data from adjacent areas, without re-training. The clustering shows a good segmentation of the magnetic anomalies into a pertinent geological map in these areas. Moreover, the first attention map isolates the structures at low scales and shows a pertinent representation of the original data. The quality of the results empirically validates our data augmentation method. Furthermore, it proves that using convolutional neural networks is pertinent for preliminary geological mapping. Thus, our method can be used in any area where a geological and petrophysical 3D model exists to train a deep learning algorithm and produce preliminary geological maps of good quality and new representations of the input data in any area sharing the same geological context, using airborne magnetic data. (github: https://github.com/MatthieuCed/GSCNN-apply-to-airborne-magnetic)