Modeling the forces during micro-milling processes is directly linked to the chip load and mechanistic model parameters that are generally dependent on the tool/work combination. Tool runout, deflection, and the material’s elastic recovery mainly affect the chip load as a function of feed. Experimentally measured micro-milling forces can be employed to identify cutting force coefficients and runout parameters. However, decoupling the interplay among runout, deflection, and elastic recovery is difficult when only measured forces are considered. In this paper, machined surface topography has been considered as an additional process output to investigate the influence of runout and deflection separately. The machined surface topography was investigated using a scanning laser microscope to identify minimum chip thicknesss and runout parameters. A finite element model of tool deflection has been developed based on the end mill geometry used in the experiments. The finite element model was used to obtain a surrogate model of the tool deflection which was implemented into the mechanistic model. Nanoindentation tests were conducted on the coated WC tool to identify its material properties which are employed in the finite element model. An uncut chip thickness model is constructed by considering preceding trochoidal trajectories of the cutting edge, helix lag, tool runout, tool deflection, and the chip thickness accumulation phenomenon. The force model was validated experimentally by conducting both slot and side milling tests on commercially pure titanium (cp-Ti). The predicted cutting forces were shown to be in good agreement with the experimental cutting forces.