Micro-milling is a mechanical microfabrication technique of removing material in micron range with a submillimeter range cutting tool. Due to the downscaling of the process, the size effect is seen as a significant hindrance that spurs higher specific cutting energy and worsens the surface quality. Further, deflection-driven vibration (transverse vibration) is critical due to the micro end mill’s small diameter, which worsens the surface quality and increases the chances of tool breakage. As a whole, size effect, and chatter can be considered the major obstacle in micro-milling. This paper adopts a novel mechanistic approach to select the machining parameters (speed, feed, and depth of cut) in micro-milling to avoid the influence of size effect and chatter. Feed per tooth is selected by considering the influence of size effect and minimum chip thickness (MUCT) on chip morphology and specific cutting energy. The depth of cut and rotational speed of the spindle is selected analytically by dynamic stability modeling and differentiating the stable and chatter zone.