Irradiating carbon nanoparticles (CNPs) with near-infrared laser beam leads to generation of heat, therefore it has potential to be used in many applications including the destruction of cancer cells. Though pulsed laser beams have been used earlier to transform shapes of metallic and semiconductor nanoparticles, changing shape of CNPs required intense electron beam irradiation. In this paper, we report significant size reduction of CNPs under continuous-wave (cw) near-infrared (NIR) laser beam micro-irradiation which was attributed to melting and vaporization or fragmentation of the carbon nanoparticles. Further, we show that the spherical shape of the CNPs can be transformed into ellipsoidal, by exposure to cw NIR laser microbeam irradiation for a few seconds. In-situ measurements using atomic force microscopy (AFM) reveal the shape and size changes of the CNPs upon laser micro-irradiation. Most importantly, cw NIR laser microbeam irradiation led to ultra-structural phase transformation of CNPs as detected via Raman spectroscopic imaging. While the graphitic CNPs could be changed to diamond-like carbon (DLC), no phase change in DLC nanoparticles was observed. These transformations did not require presence of any special chemical (catalyst, functionalization) or physical (pressure, temperature) arrangement. In-situ control of CNP-size, shape and ultra-structural properties opens new possibilities in multiple nanotechnology adventures.