We study a thermally activated on-surface planarization reaction by a detailed analysis of the reactant and reaction products from atomically resolved atomic forte microscopy (AFM), images and spectroscopy. The three-dimensional (3D) structure of the reactant, a helical diphenanthrene derivative, requires going beyond constant-height imaging. The characterization in three dimensions is enabled by acquisition and analysis of the AFM signal in a 3D data set. This Way, the structure and geometry of nonplanar molecules as well as their reaction products on terraces and at step edges can be determined.