The ability to manipulate nano-particles at the nano-scale is critical for the development of active quantum systems. This paper presents a technique to manipulate diamond nano-crystals at the nano-scale using a scanning electron microscope, nano-manipulator and custom tapered optical fibre probes. The manipulation of a approximately 300 nm diamond crystal, containing a single nitrogen-vacancy centre, onto the endface of an optical fibre is demonstrated. The emission properties of the single photon source post manipulation are in excellent agreement with those observed on the original substrate.