Cataract extraction is the most frequently performed ophthalmological procedure worldwide. Posterior capsule opacification remains the most common consequence after cataract surgery and can lead to deterioration of the visual performance with cloudy, blurred vision and halo, glare effects. Neodymium-doped yttrium aluminum garnet (Nd:YAG) laser capsulotomy is the gold standard treatment and a very effective, safe and fast procedure in removing the cloudy posterior capsule. Damaging the intraocular lens (IOL) during the treatment may occur due to wrong focus of the laser beam. These YAG-pits may lead to a permanent impairment of the visual quality. In an experimental study, we intentionally induced YAG pits in hydrophilic and hydrophobic acrylic IOLs using a photodisruption laser with 2.6 mJ. This experimental study established a novel 3D imaging method using correlative X-ray and scanning electron microscopy (SEM) to characterize these damages. By integrating the information obtained from both X-ray microscopy and SEM, a comprehensive picture of the materials structure and performance could be established. It could be revealed that although the exact same energies were used to all samples, the observed defects in the tested lenses showed severe differences in shape and depth. While YAG pits in hydrophilic samples range from 100 to 180 µm depth with a round shape tip, very sharp tipped defects up to 250 µm in depth were found in hydrophobic samples. In all samples, particles/fragments of the IOL material were found on the surface that were blasted out as a result of the laser shelling. Defects in hydrophilic and hydrophobic acrylic materials differ. Material particles can detach from the IOL and were found on the surface of the samples. The results of the laboratory study illustrate the importance of a precise and careful approach to Nd:YAG capsulotomy in order to avoid permanent damage to the IOL. The use of an appropriate contact glass and posterior offset setting to increase safety should be carried out routinely.