Within this research, a processing system is designed to enable micro scale reactions. This system includes hardware, such as microfluidic chips, its chipholder, and a controller unit, and software. The software is involved with process control and can communicate with peripheral equipment, such as pumps and analysis equipments. The discardable microchips can be designed to suit the needs of specific processes. Changing a process means changes a chip. As in all processing systems, the thermal control at all reaction positions is of utmost importance. The system's ability to maintain a certain temperature depends on accurate sensing and adequate heating and/or cooling. We have worked on determining fluid temperature in a microfluidic chip during operation. Rhodamine B, a temperature dependent fluorescent molecule, was pumped through the chip and microscopic pictures were taken. From these pictures the fluorescent intensity was calculated and correlated to the temperature. Results from practical experiments were supported by CFD models to further understand the thermal behavior. The results from our research show that running the system under normal conditions allows a stable temperature in the microfluidic chip. These moderate conditions, such as movement of air around the system and variation of fluid flow rate through the chip, have no significant effect on the temperature at reaction positions. Furthermore, the different fluid flow rates have no effect on heat up or cool down rates of the microfluidic chip. This means that the fluid temperature can be controlled, independent from practical operation. The design of the chip and the chipholder did influence the temperature distribution. The material, from which both parts are constructed, as well as the shape and position of any heating or cooling devices will have its effect. Also, the size and position of any contact between the microfluidic chip and the chipholder proved to have a profound effect on the temperature gradients over the chip. These findings indicate the importance of thermal aspects in the design of flexible process equipment on such a small scale. The results can be used to construct guidelines for designing chips and chipholders with robust temperature control possibilities.