Structural transformation of gold nanorods are investigated by high-resolution transmission electron microscopy after they have been exposed to low-energy femtosecond and nanosecond laser pulses in colloidal solution. The pulse energies were below the gold nanorod melting threshold, but allowed early stage shape transformation processes, It is found that while the as-prepared nanorods are defect-free, laser-irradiation induces point and line defects. The defects are dominated by (multiple) twins and stacking faults (planar defects), which are the precursor that drives the nanorods to convert their {110} facets into the more stable {100} and {111} facets and hence minimize their surface energy. These observations suggest that short-laser pulsed photothermal melting begins with the creation of defects inside the nanorods followed by surface reconstruction and diffusion, in contrast with the thermal melting of the rods or the bulk material, where the melting starts at the surface.