Centrifuge modelling is an established technique capable of investigating the ground’s response to complex geotechnical events. Centrifuge models are often created from reconstituted soil, with well-defined boundary conditions and known soil parameters. Clay soil models may be prepared by mixing clay powder with distilled water to form a slurry. This slurry is placed within a soil container and subjected to a vertical stress (usually in a consolidation press or consolidated inflight). This creates an isotropic model but there is a fundamental difference between this soil model and naturally occurring soil deposits. The structure and fabric present within a naturally occurring clay is not reproduced by this preparation process. It is well-established that structure and fabric in naturally deposited soils are as significant in their effect on soil behaviour as, for instance, the stress history. Inherent structure and fabric within clay soils creates anisotropy which can vary with depth, this is particularly apparent when considering the permeability. Creating a soil model for centrifuge modelling with representative permeability anisotropy would allow for a better representation of consolidation driven events and the ability to observe long-term behaviour of complex geotechnical events. Currently, there are limited methods of doing so, leading to a considerable gap in knowledge associated with the behaviour of layered ground. This paper describes the development of the equipment and experimental procedure for quantifying the structure developed by different sample preparation techniques for centrifuge modelling.