Multi-material systems interfaced with 2D materials, or entirely new 3D heterostructures can lead to the next generation multi-functional device architectures. Physical and chemical control at the nanoscale is also necessary tailor these materials as functional structures approach physical limit. 2D transition metal thiophosphates (TPS), with a general formulae Cu1-xIn1+x/3P2S6, have shown ferroelectric polarization behavior with a T c above the room temperature, making them attractive candidates for designing both: chemical and physical properties. Our previous studies have demonstrated that ferroic order persists on the surface, and that spinoidal decomposition of ferroelectric and paraelectric phases occurs in non-stoichiometric Cu/In ratio formulations. Here, we discuss the chemical changes induced by helium ion irradiation. We explore the TPS compound library with varying Cu/In ratio, using Helium Ion Microscopy, Atomic Force Microscopy (AFM), and Time of Flight-Secondary Ion Mass Spectrometry (ToF-SIMS). We correlate physical nano- and micro- structures to the helium ion dose, as well as chemical signatures of copper, oxygen and sulfur. Our ToF-SIMS results show that He ion irradiation leads to oxygen penetration into the irradiated areas, and diffuses along the Cu-rich domains to the extent of the stopping distance of the helium ions.