Diamond containing engineered color centers is rapidly becoming a medium of choice for quantum information applications. Many of the dramatic recent results in this field have been demonstrated in diamond nano-crystals. Here we demonstrate controlled synthesis of spatially isolated high quality micro- and nano-diamonds using a microwave plasma chemical vapor deposition technique (MPCVD). The growth from nano-seeds rather than other nucleation techniques allows improved control over the final size of the crystals and the density of the crystals on the substrate. The growth rate of the diamond crystals was found to be 22 nm/min. Various parameters of the growth sequence were studied and the microwave power density was found to have the major influence on the crystal morphology, with the best quality diamond formed under conditions of relatively high pressure and plasma density. Our ability to control size, dispersion and levels of perfection constitutes an enabler for future quantum information applications utilizing diamond color centers.