The main purpose of this study strongly concerned micro machining error estimation by using FEM analysis of tool deflection shapes in micro flat end-milling process. For the precision micro flat end-milling process, analysis of micro cutting errors is mandatory. In general, tool deflection is a major factor which causes cutting error and limits realization of the high-precision cutting process. Especially, in micro end-milling process, micro tool deflection generates very serious problems in contrast to macro tool deflection. Methods which deal with compensation of cutting error by tool deflection in macro end-milling process have been studied plentifully but, few researches transact with micro scaled cutting tool deflection in micro cutting process. Therefore, the trend of micro tool deflection was estimated by using FEM analysis in this paper. Cutting forces were acquired by micro dynamometer and these were utilized in FEM analysis. In order to verify FEM analysis results, micro machining processes were carried out and real machined profiles were compared with FEM results. Finally through the proposed approach well suited FEM results were obtained.