This article presents an investigation of the machining response of metallurgically and mechanically modified materials at the micro-scale. Tests were conducted that involved micro-milling slots in coarse-grained Cu99.9E with an average grain size of 30 µm and ultrafine-grained Cu99.9E with an average grain size of 200 nm, produced by equal channel angular pressing. A new method based on atomic force microscope measurements is proposed for assessing the effects of material homogeneity changes on the minimum chip thickness required for a robust micro-cutting process with a minimum surface roughness. The investigation has shown that by refining the material microstructure the minimum chip thickness can be reduced and a high surface finish can be obtained. Also, it was concluded that material homogeneity improvements lead to a reduction in surface roughness and surface defects in micro-cutting.