Micro end-milling has been becoming an important machining process to manufacture a number of small products such as micro-devices, bio-chips, micro-patterns and so on. Despite the importance of micro end-milling, many related researches have given grand efforts to micro end-milling phenomenon, for example, micro end-milling mechanism, cutting force modeling and machinability. This paper strongly concerned actual problem, micro tool deflection, which causes excessive machining errors on the workpiece. To solve this problem, machining error prediction method was proposed through a series of test micro cutting and analysis of their SEM images. An iterative algorithm was applied in order to obtain corrected tool path which allows reducing machining errors in spite of tool deflection. Experiments are carried out to validate the proposed approaches. In result, remarkable error reduction could be obtained.