A method for making low emissivity panels, including control the ion characteristics, such as ion energy, ion density and ion to neutral ratio, in a sputter deposition process of a layer deposited on a thin conductive silver layer. The ion control can prevent or minimize degrading the quality of the conductive silver layer, which can lead to better transmittance in visible regime, block more heat transfer from the low emissivity panels, and potentially can reduce the requirements for other layers, so that the overall performance, such as durability, could be improved.