Serial section reconstruction is widely used for visualising complex three-dimensional objects, but little research has been applied to modelling geoscientific applications. We review previous work and highlight the correspondence problem, particularly important in reconstructions from geoscientific data. We propose an automatic solution to the correspondence problem, based on a minimum-spanning-tree algorithm. The improved results stem from the use of topological information to help decide which edges appear in the final correspondence graph. We then reconstruct some invertebrate fossil samples, before outlining future possibilities in deriving solutions for complex samples, using richer information for each specimen.