The present disclosure relates to novel microwave systems and new applications of microwave in medical, chemical and materials manufacturing and processing, food and health industries as well as analytical chemistry instrumentation for in situ study of microwave effects. In the case of medical applications, the microwave based damage is conducted in a way to diminish ablating or damaging the collateral issue and to increase the probability of procedure achievement. It comprises adjusting the variable length microwave pulse, pulse sequence, pulse shapes, and using phase encoding and the active cooling of the target and its surrounding dependent on the measured temperature to achieve a desired temperature.