Infrared thermography technology has improved drastically in recent years and is regaining interest in medicine for applications such as deep inferior epigastric perforate flap breast reconstruction, breast cancer diagnosis, skin tissue identification, psoriasis detection, etc. However, there is still a need for an optimised measurement setup and protocol in order to capture the most suitable images for decision making and further processing. Nowadays, different cooling methods are being used; nevertheless, a general optimised cooling protocol is not yet defined. In this manuscript, several cooling techniques, as well as the measurement setups, are reviewed and optimised. It is possible to enhance the thermal images by selecting an appropriate cooling method and duration, and additionally, an optimised measurement setup enables a comparison between different inspections.