We report the fabrication and structural study of TiO2 nanopillar arrays produced by two-step anodization of Al/TiN bilayer (1000 nm/250 nm). The as-prepared nanopillars are amorphous; their structural evolution was investigated upon air annealing in the 300–800 °C range. Annealing at 300 °C initiates crystallization, at 500 °C predominantly nanocrystalline anatase is formed, while at 800 °C grain growth and coexistence of anatase and rutile are observed. The array morphology (diameter ~20 nm, pitch ~50 nm, height ~150 nm) remains intact even after high-temperature treatment. These results indicate that ~500 °C is an optimal annealing condition to obtain pure anatase while preserving the nanostructured geometry, which is important for photocatalytic applications and for using TiO2 nanopillar arrays as platforms for hybrid SERS-substrates.