With semiconductor-device geometry shrinking and becoming more complex, highly diluted chemicals are used during aqueous silicon wafer cleaning. The use of physical cleaning aids such as megasonic agitation with dilute chemistry or high-pressure atomizing jet sprays to avoid reduction of particle removal efficiency is prone to cause structural damage to both fragile freestanding MEMS and high-aspect-ratio LSI structures. The surface tension of water can also cause pattern collapse of nano-structures. In addition to this, ultra-pure water can cause several other problems resulting in the degradation of device characteristics. These problems make the development of novel damage free non-aqueous cleaning methods a high priority. In this paper, several water-caused problems to bring damage to silicon devices are discussed with some possible solutions and, as the ultimate solutions to overcome the shortcomings of water-based cleaning, various alternative damage-free non-aqueous cleaning techniques are overviewed and discussed, which include low pressure, elevated temperature HF vapor cleaning, cryogenic aerosol nitrogen cleaning, supercritical carbon dioxide cleaning, and pinpoint dry cleaning that employs lasers, nano-probes, or nano-tweezers. There will be more research challenges and opportunities in these environmentally-benign damage-free cleaning technologies in the near future.