To allow researchers to fabricate micro- and nano-devices on a small scale, without having to use complex cleanroom facilities, a single tool is proposed in which a variety of typical cleanroom techniques and processes is combined. This ‘cleanroom’ in SEM tool, based on a scanning electron microscope (SEM), integrates several add-on tools, such as a miniature plasma source for sputtering and cleaning purposes, a miniature thermal evaporator for metal deposition, and facilities to enable in-situ selective atomic layer deposition. The cleanroom techniques and processes selected for integration in the ‘cleanroom’ in SEM tool are discussed, and the design and fabrication of the add-on tools are presented. Finally the proofs of principle of the plasma source, evaporator and in-situ selective ALD process are experimentally demonstrated.