Established laser-based ionization experiments require the surface of a sample to be as flat as possible to guarantee optimal laser focus. A laser ablation electrospray ionization (LAESI) source was custom-built to accommodate the topography of non-flat sample surfaces. Employing a confocal distance sensor, a height profile of the surface in question was recorded prior to the actual ionization experiment. The robustness of the system was evaluated by the metabolic profiling of radish (Raphanus sativus) leaves, chosen due to their pronounced surface features and known content of specialized metabolites. After the ionization experiments, light microscopy imaging was performed to evaluate ablation crater size and position. Reproducible ablation mark diameters of 69 ± 7 μm in average have been achieved. Mass spectrometric imaging capability has been proven on R. sativus leaf samples as well.