Ferroelectrics nanostructures with dimensions below 1µm are key building blocks for enabling future integration of ferroelectrics into nanoelectronic devices but are still yet rarely studied. Here, we investigate helium and neon ion milling of BaTiO3 single crystals in order to prepare BaTiO3 nanorods and nanodisks of ~sub-500 nm dimensions. We study the strain and the polar domain orientation in the nanostructures. Nanopillars with different aspect ratios were fabricated in BaTiO3 (100) and (001) single crystals using either helium or neon ion milling with different processing conditions in a Zeiss Orion NanoFab microscope. We typically prepared cylinders with diameter of ~ 200 nm and with a height at least twice as small or as large as the diameter. For these dimensions, Ne+ ions are used first and He+ ions can be used subsequently for a fine adjustment of the final size. We will first discuss the effect of milling parameters on the control of the shape and size of the nanostructures. Then we will discuss the crystalline structure, strain and defects resulting from the ion milling. The pillars were analyzed by polarized Raman spectroscopy and scanning transmission electron microscopy (STEM). The comparison of Raman spectra with those of the bulk crystals show that there is an impact of the ion milling on the crystal orientation. For the nanostructures fabricated on BaTiO3 (001) and BaTiO3 (100) single crystals, there is evidence that an increase in aspect ratio leads to an increase in the proportion of a- and c-orientated domains, respectively. The information gained from the STEM and from geometrical phase analysis of HAADF images will be discussed, emphasizing the effect of the dimensions on the strain state. Finally, the potential damages caused by the ions during the milling processing will be evaluated. We show that the nanofabrication by neon ion milling is an effective method that could be used for the rapid prototyping of nanoscale device building blocks.