We study the behavior of the organic material (TMTSF)2PF6 (TMTSF: tetramethyl tetraselena fulvalene) under focused Ga+ ion beam impact using conducting probe atomic force microscopy (CP-AFM) and secondary ion mass spectrometry. The (TMTSF)2PF6 crystals are exposed to a 25 keV focused ion beam with the sample native surface both perpendicular and slightly tilted to the incident beam axis, where drastically different etching effects are observed. Moreover, very large ion implantation depth, as compared to conventional substrates, is obtained when the sample surface is set perpendicular to the beam axis, while the implantation depth is much smaller at the tilted angle. This phenomenon is discussed in relation with the sample structure anisotropy. Finally, the transport property modifications of the impact areas are investigated by CP-AFM and discussed in relation with both the crystalline structure and the polarizability of the matrix.