A micro channel device processing apparatus includes a heating/cooling chamber configured to receive at least a sub-portion of a micro channel device and a fluid control system that controls a flow of a heating/cooling fluid in the chamber. A method includes controlling a temperature of a sample carried by a micro channel device installed in a micro channel device processing apparatus via a heating/cooling chamber of the processing apparatus. A micro channel device processing apparatus includes a heating/cooling chamber configured to receive a micro channel device carrying a sample and means for controlling a temperature of the sample in the chamber.