The micro milling operation is one of the manufacturing processes, which can produce 3D parts in the range of less than a millimetre. Miniaturization of components results in increasing the ratio of surface area to volume of components, which in turn increases the role of surface on the component performance. Therefore, anticipating the relationship between micro milling parameters and surface roughness is of extreme importance. In this paper, a model is proposed which combines the geometric profile of tool end and coordinates of the major cutting edge, which is able to anticipate the profile and surface roughness of the groove floor. The micro-end-mill geometry is considered in macro and micro scales. Relationship between the major cutting edge coordinates and tool profile are derived. Introducing different cutting mechanisms in micro milling operation, effect of different factors such as elastic recovery, and minimum chip thickness, are considered for calculating surface roughness. Feed effect, end edge radius, and effect of minimum chip thickness on surface roughness are investigated for Stainless Steel 316 using the performed simulation of MATLAB software. Moreover, micromilling operation results of the proposed model were compared with experimental results, and correctness of the simulation was validated. In addition, effects of feed per tooth on surface roughness and chip formation were also investigated.