This paper presents a machining error compensation methodology due to deflection of micro cutting tools in side cutting processes. Generally in order to compensate for tool deflection errors it is necessary to carry out a series of simulations, cutting force prediction, tool deflection estimation and compensation method. These can induce numerous calculations and expensive costs. This study proposes an improved approach which can compensate for machining errors without simulation processes concerning prediction of cutting force and tool deflection. Based on SEM images of test cutting specimens, polynomial relationships between machining errors and corrected tool positions were induced. Taking into account changes of cutting conditions caused by tool position variation, an iterative algorithm was applied in order to determine corrected tool position. Experimental works were carried out to validate the proposed approach. Comparing machining errors of nominal cutting with those of compensated cutting, overall machining errors could be remarkably reduced.