Thermoplastic materials hold great promise for next-generation engineered and sustainable plastics and composites. However, due to their thermoplastic nature and viscoplastic material response, it is difficult to predict the properties of surfaces generated by machining. This is especially problematic in micro-channel machining, where burr formation and excessive surface roughness lead to poor component-surface integrity. This study attempts to model the influence of size effects, which occur due to the finite sharpness of any cutting tool, on surface finish and burr formation during micro-milling of an important thermoplastic material, polycarbonate. Experimental results show that the depth of cut does not affect either surface finish or burr formation. A proposed new sideflow model shows the dominant effect of cutting-edge radius and feed rate on surface finish, while tool edge roughness, coating and feed rate have the most pronounced influence on burr formation. Overall, a good agreement between the experimental data and the proposed size effect model for the machining of thermoplastic material was found. Based on these results, tool geometry and process parameters may be optimized for improved surface integrity of machined thermoplastic components