The field of metrology, which focuses on the scientific study of measurement, is grappling with a significant challenge: predicting the measurement accuracy of sophisticated 3D scanning devices. These devices, though transformative for industries like manufacturing, construction, and archeology, often generate complex point cloud data that traditional machine learning models struggle to manage effectively. To address this problem, we proposed a PointNet-based model, designed inherently to navigate point cloud data complexities, thereby improving the accuracy of prediction for scanning devices’ measurement accuracy. Our model not only achieved superior performance in terms of mean absolute error (MAE) across all three axes (X, Y, Z) but also provided a visually intuitive means to understand errors through 3D deviation maps. These maps quantify and visualize the predicted and actual deviations, which enhance the model’s explainability as well. This level of explainability offers a transparent tool to stakeholders, assisting them in understanding the model’s decision-making process and ensuring its trustworthy deployment. Therefore, our proposed model offers significant value by elevating the level of precision, reliability, and explainability in any field that utilizes 3D scanning technology. It promises to mitigate costly measurement errors, enhance manufacturing precision, improve architectural designs, and preserve archeological artifacts with greater accuracy.