Indium-based micro-bump arrays, among other things, are used for the bonding of infrared photodetectors and focal plane arrays. In this paper, several aspects of the fabrication technology of micrometer-sized indium bumps with a smooth surface morphology were investigated. The thermal evaporation of indium has been optimized to achieve ~8 μm-thick layers with a small surface roughness of Ra = 11 nm, indicating a high packing density of atoms. This ensures bump uniformity across the sample, as well as prevents oxidation inside the In columns prior to the reflow. A series of experiments to optimize indium bump fabrication technology, including a shear test of single columns, is described. A reliable, repeatable, simple, and quick approach was developed with the pre-etching of indium columns in a 10% HCl solution preceded by annealing at 120 °C in N2.