The recent technological progressions in industries have offered ascent to the continually growing requests for microstructures, sensors, and parts. Micro-milling is a promising method to create these scaled down structures, sensors, and parts. Yet, micro-milling still confronts some significant difficulties, tormenting further provision of this innovation. The most noticeable around them is micro burr formation. Burrs created along the completed edges and surfaces in micro-milling operation have huge effect on the surface quality and performance of the completed parts and microstructures. In any case, deburring of micro-parts is not conceivable because of bad accessibility and tight tolerances in micro segments. One of the methods to minimize micro burr formation in micro milling is by enhancing the geometry of the device. As minimization of micro burrs still remains a key test in micro machining, not many researchers have worked in this field. The main aim of the research work is to present finite element analysis of flat end mill micro cutters used in micro milling by varying geometry of the tools. Apart from this, study has been done in detail on burr formation in micro milling and what factors affect it. Burr formation simulation has been carried out while varying the tool geometry.