The interaction of geological structures at different scales often results in complex three-dimensional geometries. This can especially be the case when interpreting progressively deformed multi-layer fold systems which can result in complex non-cylindrical geometries of varying scale and congruity. Curvature analysis methods have lately been developed to assist this for analysing three-dimensional geological surfaces which do not need to assume cylindricity, but these methods are often applied to three-dimensional seismic horizons which have specific considerations that can affect scale analysis. We show how the application of manifold harmonic analysis together with implicit geological modelling can assist in the interpretation of fold structures. This is demonstrated by developing a three-dimensional model of the Padtherung Syncline, central Hamersley province, Western Australia, and applying our manifold harmonic analysis methods. Our results show how the analysis can be used as evidence to re-interpret the polyclinal structure as progressively deformed rather than a superposed structure.