Microwave annealing (MWA) and rapid thermal annealing (RTA) of dopants in implanted Si are compared in their abilities to produce very shallow and highly activated junctions. First, arsenic (As), phosphorus (P), and B 2 implants in Si substrate were annealed by MWA at temperatures below 550 °C. Next, enhancing the substitutional carbon concentration ([C] sub ) by cluster carbon implantation in (100) Si substrates with MWA or RTA techniques was investigated. Annealing temperatures and time effects were studied. Different formation mechanisms of SiC x layer were observed. In addition, substrate temperature is an important factor for dopant activation during MWA and in situ doped a-Si on oxide/Si substrate or glass were compared to elucidate the substrate temperature effect. After the discussion of dopant activation in Si substrates, low temperature formation of ultrathin NiGe layer is presented. Ultrathin NiGe films with low sheet resistance have been demonstrated with a novel two-step MWA process. In the two-step MWA process, the first step anneals the sample with low power MWA, and the second step applies higher power MWA for reducing sheet resistance. During fixed-frequency microwave heating, standing wave patterns may be present in the MWA chamber resulting in nodes and antinodes and thermal variations over the process wafer. Therefore, the effects of Si or quartz susceptor wafers on dopant activation and sheet resistance uniformity during fixed-frequency MWA were investigated.