We have developed a new Reverse Monte Carlo code, called the micro Reverse Monte Carlo (m-RMC), which is applicable to structure analysis of nanomaterials and surface species. In the m-RMC, Reverse Monte Carlo is applied to an ensemble of replica files, each of which contains one molecule or one small cluster, because the Extended X-ray Absorption Fine Structure (EXAFS) is sensitive to short-range structures and has negligible interaction between molecules or clusters. We apply the m-RMC to face-centered cubic metals (Cu, Pd, and Pt) and discuss the advantages, validation, and problems of the m-RMC. The bond distance and some cumulant coefficients can be determined from the EXAFS using m-RMC. Some 50-100 replica files are sufficient to reproduce the EXAFS oscillations and radial distributions. The bond distance can be determined, including the asymmetric distributions,by m-RMC. We also apply m-RMC to α-MoO₃ and Au clusters. The m-RMC analysis of MoO₃ shows that three radial distribution peaks appear corresponding to three types of Mo–O bonds. The m-RMC analysis of Au cluster indicates the presence of Au₅₅ cuboctahedral structure with Au-Au distance at 0.288 nm. We obtain a 3 D image of Au₅₅ nanocluster from the unified file. The m-RMC method can be applied to the analysis of the EXAFS for chemical systems with appropriate care. [DOI: 10.1380/ejssnt.2014.322]