The invention provides methods and systems that control the application of a material onto micro-rough implant surfaces. Thus, the present invention provides method of applying crystalline nanoparticles onto the surface of an implant to produce an implant with a crystalline nanoparticle layer on its surface, the method comprising: providing an implant substrate body; applying crystalline nanoparticles onto the surface of the implant; and rotating the implant, to produce an implant with a crystalline nanoparticle layer on its surface. This method of nanoparticle application is designed to promote the integration of implants, such as dental and orthopedic screws, into living tissue, and offers the ability to control the thickness and uniformity of the nanoparticle layer, in one or several layers, while simultaneously retaining the microroughness of the implant. Further provided are systems for applying crystalline nanoparticles onto the surface of an implant and implants having a crystalline nanoparticle layer on their surfaces.