CdS/CdTe heterojunction was subjected to chemical treatment commonly used in photovoltaic device fabrication to determine the resulting microscopic effect on the morphology and structure. CdS and CdTe thin films were electrodeposited successively onto indium tin oxide (ITO) from aqueous solution. Containing CdCl₂ and Na₂S₂O₃ for the deposition of thin film windows, the ITO/CdS resulting substrates was then used for the deposition of CdTe thin film absorber using aqueous solution of CdSO₄ and TeO₂. Next CdCl₂ dip followed by 400°C heat treatment was used to modify the CdTe/CdS surface and interface. Scanning electron microscopy (SEM) and Atomic force microscopy (AFM) were used to evaluate the resulting surface morphology. X-ray diffraction analysis reveals that the heat treatment enhances the recrystallisation and shifts the CdTe peaks towards a smaller lattice parameter.