We demonstrate a method for engineering niobium selenide (Nb-Se) nanostructures by systematically adjusting the growth parameters in a bottom-up chemical vapor transport (CVT) process, and study their influence on the feature of the resulting products, such as composition, morphology and phase. Thermodynamic calculations were performed to optimize the growth process. Using either, I₂ or NbCl₅ as transport agent resulted in the formation of high quality NbSe₂ nanocrystals or Nb₂Se₉ nanowires respectively. Different growth temperatures lead to formation of NbSe₂ at ( T ₁ = 1000 °C, T ₂ = 800 °C) and (NbSe₄)₃I at ( T ₁ = 600 °C, T ₂ = 400 °C). This study explored also the effect of the amount of transport agent as well as the nature and the pre-growth thermal oxidation duration of the substrates on the morphology, the growth mode and the distribution of the deposited crystals over the substrates. The chemical composition and morphology of the nanocrystals were analyzed by energy dispersive X-ray spectroscopy, scanning electron microscopy, atomic force microscopy and Raman spectroscopy. The high crystalline quality was confirmed by high-resolution transmission electron microscopy. Charge transport measurements of metallic NbSe₂ nanostructures revealed a small excess resistance below 6.5 K, attributed to inhomogeneous superconductivity, due to either local charge puddles or to quantum fluctuations in highly-crystalline 2D superconductors. Nb₂Se₉ nanowires were found insulating.