Rapid advances in nanoscience rely on continuous improvements of material manipulation at near-atomic scales. Currently, the workhorse of nanofabrication is resist-based lithography and its various derivatives. However, the use of local electron, ion, and physical probe methods is expanding, driven largely by the need for fabrication without the multistep preparation processes that can result in contamination from resists and solvents. Furthermore, probe-based methods extend beyond nanofabrication to nanomanipulation and to imaging which are all vital for a rapid transition to the prototyping and testing of devices. In this work we study helium ion interactions with the surface of bulk copper indium thiophosphate CuMIIIP2X6 (M = Cr, In; X= S, Se), a novel layered 2D material, with a Helium Ion Microscope (HIM). Using this technique, we are able to control ferrielectric domains and grow conical nanostructures with enhanced conductivity whose material volumes scale with the beam dosage. Compared to the copper indium thiophosphate (CITP) from which they grow, the nanostructures are oxygen rich, sulfur poor, and with virtually unchanged copper concentration as confirmed by energy-dispersive X-ray spectroscopy (EDX). Scanning electron microscopy (SEM) imaging contrast as well as scanning microwave microscopy (SMM) measurements suggest enhanced conductivity in the formed particles, whereas atomic force microscopy (AFM) measurements indicate that the produced structures have lower dissipation and are softer as compared to the CITP.