Galvanometric laser scanner (GLS) systems are widely used for materials processing due to their high precision, processing velocity, and repeatability. However, GLS systems generally suffer from scan field distortions due to joint and task space relationship errors. The problem is further pronounced in robotic applications, where the GLS systems are manipulated in space, as unknown errors in the relative pose of the GLS can be introduced. This paper presents an in situ, data-driven methodology for calibrating GLS systems using 3D scanning, emphasising the flexibility, generalisation, and automated industrial integration. Three-dimensional scanning serves two primary purposes: (1) determining the relative pose between the GLS system and the calibration plate to minimise calibration errors and (2) supplying an image processing algorithm with dense and accurate data to measure the scan field distortion based on the positional deviations of marked fiducials. The measured deviations are used to train a low-complexity Radial Basis Function (RBF) network to predict and correct the distorted scan field. The proposed method shows promising results and significantly reduces the scan field distortion without the use of specialised calibration tools and with limited knowledge of the optical design of the GLS system.