Physical analogue models, commonly known as “sand boxes,” help understanding structural geological deformational processes. Medical-type CT X-ray scanning is a proven method employed for monitoring the internal deformation of sand boxes in space and time. However, standard 4D reconstruction approaches of acquired CT scans (including digital volume correlation techniques) do not always enable an accurate monitoring and analysis of the strain patterns when deformation is highly non-cylindrical, non-coaxial or rotational. In this contribution, we focus on the use of highly absorbent X-ray markers as novel materials to obtain more accurate 4D monitoring in analogue models. We show how to optimize the type and proportion of linear and dispersed markers with respect to standard sand. We demonstrate that red lead or iron powders produce sufficient brightness to be used as markers to image internal deformation in the radiograms and enabling to be detected in standard imaging files, which will fundamental for the application of digital image correlation techniques in the aforementioned settings. Few preliminary experiments are shown to assess the applicability of the methodology in sand boxes together with the statement of some future challenges and developments.