In this paper, we present a new method for virtual restoration of digitized paintings, with the special focus on the Ghent Altarpiece (1432), one of Belgium’s greatest masterpieces. The goal of the work is to remove cracks from the digitized painting thereby approximating how the painting looked like before ageing for nearly 600 years and aiding art historical and palaeographical analysis. For crack detection, we employ a multiscale morphological approach, which can cope with greatly varying thickness of the cracks as well as with their varying intensities (from dark to the light ones). Due to the content of the painting (with extremely many fine details) and complex type of cracks (including inconsistent whitish clouds around them), the available inpainting methods do not provide satisfactory results on many parts of the painting. We show that patch-based methods outperform pixel-based ones, but leaving still much room for improvements in this application. We propose a new method for candidate patch selection, which can be combined with different patch-based inpainting methods to improve their performance in crack removal. The results demonstrate improved performance, with less artefacts and better preserved fine details.