During work on homogenisation treatments of 6063 Aluminium Alloy extrusion billets, there was a concern on an insufficient temperature distribution data from the originally positioned thermocouples. Since the furnace had been in regular use, for sometime, it was decided to use additional thermocouples to obtain more reliable pictures of temperature distribution. Heat flow and 3D temperature distribution within the furnace were simulated to optimize thermocouple positioning, especially at different positions within the furnace load of billets. The simulation also highlighted the need for improvements in the insulating system and in the heating arrangement in the furnace. The results on aluminium samples were examined via an image analysis technique to quantify the precipitated phases in the microstructure. This, in turn, has led to less variation in the homogenisation of billets from different positions in the furnace load and hence more consistent microstructures after the heat treatment.