Direct nano-scale microanalysis is important for photovoltaic functional thin films to characterize their homogeneity and purity. This demands combining spatial resolution in the micro/nano-scale and sensitivity in the trace-level range, which is at the moment beyond state-of-the-art. As dictated by counting statistics, the reduction of the spot size degrades the detection limit. The utilization of a tabletop XUV laser at λ = 46.9 nm has shown to dramatically improve the ablation efficiency with respect to that of visible lasers, such that ablation spot of 1 μm limits. Li-doped Cu 2 ZnSn(S,Se) 4 (so-called kesterite) thin films were irradiated across 3D ablation arrays for hyperspectral mapping by means of time-of-flight mass spectrometry. The nominal 3D data node lattices were the initialisation perceptron, filled with measured values, and for a detailed supervised learning postprocessing, the node-to-node links were analysed by means of a 2D-kernel covariance algorithm. The latter permitted to obtain robust 3D elemental distribution functions well below the measurement spacing, giving insights into the inhomogeneity and impurities.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.