In this chapter, the wavefunction analysis is demonstrated, applied to the organic charge transfer salts composed of electron donor and electron acceptor molecules. Scanning tunneling microscopy (STM) images of the surface donor layers in the three charge transfer salts, α-(BEDT-TTF) 2 I 3 , β-(BEDT-TTF) 2 I 3 , and (EDO-TTF) 2 PF 6 , are analyzed with the atomic π electron orbitals of sulfur, oxygen, and carbon atoms. We have deduced three different kinds of surface molecular reconstructions as follows: (1) charge redistribution in α-(BEDT-TTF) 2 I 3 , (2) translational reconstruction up to 0.1 nm in β-(BEDT-TTF) 2 I 3 , and (3) rotational reconstruction transforming the 1D axis from the a axis to the b axis in (EDO-TTF) 2 PF 6 . Finally, it is concluded that the surface reconstruction is ascribed to the additional gain of the cohesive energy of the π electron system, provoked by the reduced steric hindrance with the anions of the missing outside double layer. The investigations of the surface states provide not only interesting behaviors of the surface cation layer, but also important insights into the electronic states of a lot of similar charge transfer crystals, as demonstrated in α-(BEDT-TTF) 2 I 3 .