This work reports on the investigation of homogeneity of the inside of indium micro-bumps/ columns placed on Ti/Pt/Au under bump metallisation. This is very important for connection resistivity, long-time durability, and subsequent hybridisation process (e.g., die-bonding). Gold reacts with indium to form intermetallic alloys with different chemo-physical parameters than pure indium. The geometrical and structural parameters of intermetallic alloys were analysed based on transmission electron microscope images. Distribution of elements in the investigated samples was determined using the transmission electron micro-scope with energy dispersive spectroscopy method. A thickness of intermetallic alloy was 1.02 μm and 1.67 μm in non-annealed (A) and annealed (B) indium columns, respectively. The layered and column-like interior structure of alloys was observed for both samples, respectively, with twice bigger grains in sample B. The graded chemical composition of Au-In intermetallic alloy was detected for the non-annealed In columns in contrast to the constant composition of 40% of Au and 60% of In for the annealed sample B. The atomic distribution has a minor impact on the In column mechanical stability. A yield above 99% of an In column with a 25 µm diameter and a 11 µm height is possible for a uniform columnar structure of intermetallic alloy with a thickness of 1.67 μm.