Visual light photography, infrared reflectography, ultraviolet fluorescence photography and x-radiography reveal even hidden compositional layers in paintings. To investigate the connections between these images, a multi-modal registration is essential. Due to varying image resolutions, modality dependent image content and depiction styles, registration poses a challenge. Historical paintings usually show crack structures called craquelure in the paint. Since craquelure is visible by all modalities, we extract craquelure features for our multi-modal registration method using a convolutional neural network. We jointly train our keypoint detector and descriptor using multi-task learning. We created a multi-modal dataset of historical paintings with keypoint pair annotations and class labels for craquelure detection and matching. Our method demonstrates the best registration performance on the multi-modal dataset in comparison to competing methods.