Mechanical alloying and mechanochemical treatment are the major powder processing techniques on the nano scale. In these processes a high energy ball mill has been applied to synthesize compounds and nanocomposites such as aluminum metal matrix nanocomposite, hydroxyapatite and bionanocomposites based on hydroxyapatite. These processes involve deformation, cold welding, fracturing, and rewelding of powder particles. Due to the applied mechanical forces, chemical reactions and phase transformations could also take place. In the present research work, the effects of milling time, milling media, and sonication process on the microstructures and morphology of the obtained materials were evaluated by X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM), and Transmission Electron Microscopy (TEM). The results indicate that increasing the milling time leads to an increased lattice strain and decreased crystallite sizes. Furthermore, the results show that the sonication process leads to the morphological improvement of nanocrystalline hydroxyapatite. The obtained data show that the nanocrystalline hydroxyapatite with low contamination and suitable morphology can be produced in Polyamide6 vials similar to stainless steel vials, therefore it seems that using polymeric and polymeric based nanocomposite vials with high strength and wear resistance could lead to a new way for the mass production of nanocrystalline hydroxyapatite with high performance, low contamination and low cost.