Multi-layer images are currently the most prominent scene representation for viewing natural scenes under full-motion parallax in virtual reality. Layers ordered in diopter space contain color and transparency so that a complete image is formed when the layers are composited in a view-dependent manner. Once baked, the same limitations apply to multi-layer images as to conventional single-layer photography, making it challenging to remove obstructive objects or otherwise edit the content. Object removal before baking can benefit from filling disoccluded layers with pixels from background layers. However, if no such background pixels have been observed, an inpainting algorithm must fill the empty spots with fitting synthetic content. We present and study a multi-layer inpainting approach that addresses this problem in two stages: First, a volumetric area of interest specified by the user is classified with respect to whether the background pixels have been observed or not. Second, the unobserved pixels are filled with multi-layer inpainting. We report on experiments using multiple variants of multi-layer inpainting and compare our solution to conventional inpainting methods that consider each layer individually.