Nanomaterials have attracted great interest due to the unique physical properties and great potential in the applications of nanoscale devices. Two dimensional atomic crystals, which are atomic thickness, especially graphene, have triggered the gold rush recently due to the fascinating high mobility at room temperature for future electronics. The crystal structure of nanomaterials will have great influence on their physical properties. Thus, this thesis is focused on developing the methods to control the crystal structure of nanomaterials, namely quantum dots as semiconductor, boron nitride (BN) as insulator, graphene as semimetal, with low cost for their applications in photonics, structural support and electronics. In this thesis, firstly, Mn doped ZnSe quantum dots have been synthesized using colloidal synthesis. The shape control of Mn doped ZnSe quantum dots has been achieved from branched to spherical by switching the injection temperature from kinetics to thermodynamics region. Injection rates have been found to have effect on controlling the crystal phase from zinc blende to wurtzite. The structural-property relationship has been investigated. It is found that the spherical wurtzite Mn doped ZnSe quantum dots have the highest quantum yield comparing with other shape or crystal phase of the dots. Then, the Mn doped ZnSe quantum dots were deposited onto the BN sheets, which were micron-sized and fabricated by chemical exfoliation, for high resolution imaging. It is the first demonstration of utilizing ultrathin carbon free 2D atomic crystal as support for high resolution imaging. Phase contrast images reveal moiré interference patterns between nanocrystals and BN substrate that are used to determine the relative orientation of the nanocrystals with respect to the BN sheets and interference lattice planes using a newly developed equation method. Double diffraction is observed and has been analyzed using a vector method. As only a few microns sized 2D atomic crystal, like BN, can be fabricated by the chemical exfoliation. Chemical vapour deposition (CVD) is as used as an alternative to fabricate large area graphene. The mechanism and growth dynamics of graphene domains have been investigated using Cu catalyzed atmospheric pressure CVD. Rectangular few layer graphene domains were synthesized for the first time. It only grows on the Cu grains with (111) orientation due to the interplay between atomic structure of Cu lattice and graphene domains. Hexagonal graphene domains can form on nearly all non-(111) Cu surfaces. The few layer hexagonal single crystal graphene domains were aligned in their crystallographic orientation over millimetre scale. In order to improve the alignment and reduce the layer of graphene domains, a novel method is invented to perform the CVD reaction above the melting point of copper (1090 ºC) and using molybdenum or tungsten to prevent the balling of the copper from dewetting. By controlling the amount of hydrogen during the growth, individual single crystal domains of monolayer over 200 µm are produced determined by electron diffraction mapping. Raman mapping shows the monolayer nature of graphene grown by this method. This graphene exhibits a linear dispersion relationship and no sign of doping. The large scale alignment of monolayer hexagonal graphene domains with epitaxial relationship on Cu is the key to get wafer-sized single crystal monolayer graphene films. This paves the way for industry scale production of 2D single crystal graphene.