We report a description of the SiC(0001) 3 x 3 silicon carbide reconstruction based on single-molecule scanning tunneling microscopy (STM) observations and density functional theory calculations. We show that the SiC(0001) 3 x 3 reconstruction can be described as contiguous domains of right and left chirality distributed at the nanoscale, which breaks the to date supposed translational invariance of the surface. While this surface heterochirality remains invisible in STM topographies of clean surfaces, individual metal-free phthalocyanine molecules chemisorbed on the surface act as molecular lenses to reveal the surface chirality in the STM topographies. This original method exemplifies the ability of STM to probe atomic-scale structures in detail and provides a more complete vision of a frequently studied SiC reconstruction.