Pure Sn solder balls of initial diameter of 2 mm, having been reflow soldered on Cu substrate at 573.15 K for 1, 2 and 5 min, were subjected to furnace cooling. Upon the start of reflow, the initially spherical solder balls underwent a rapid radial spreading and wetting on Cu substrate and thus attained non-spherical geometry with a maximum height at the center whereas a minimum one at the periphery. The wetting or interfacial reaction, that would produce an even scalloped intermetallic compounds (IMCs) during isothermal reflow, resulted in the growth of dense prismatic IMC rods at the central region during cooling whereas the peripheral scalloped IMCs were not overriden by the faceted or prismatic rods during the temperature reduction procedure. Reduced interfacial heat transfer at the central interface, existence of radial isotherms and lowered supply of Cu precipitates at the peripheral interface owing to the compromised solder height have been discussed as the factors responsible for the segregated IMC morphology. The abundant precipitation of Cu and the presence of thermal gradient, sustain a screw dislocation based growth of hexagonal IMC whiskers. The increase in reflow duration is associated with the enhanced tubularity of the rods. Finite element method has been utilized to accomplish numerical simulations for heat and mass transfer in solder phase as well as for anisotropic thermal conduction at the dislocation in evolving IMC.