This article is focused on the analysis of the structure-process relationships of biodegradable materials. It is mainly focused on the analysis of phase separation phenomenon occurring during the extrusion of plasticized starch/polycaprolactone blends, in a slit die. Rheological characterizations are carried out, in-line in an instrumented slit die at the exit of the extruder and, out-line with different rheometers. In certain conditions, a pseudo-multilayer structure can be generated with a polyester rich skin. Then, Electron Spectroscopy for Chemical Analysis (ESCA) and Fourier Transformed Infrared Attenuated Total Reflectance (FTIR-ATR) analyses are conducted to evaluate semi-quantitatively the polyester surface enrichment. In the range of available shear rates, the phase separation is mainly driven by the molecular weight of polycaprolactone, linked to its molten state viscosity. Three zones of surface enrichment, dependent on the molecular weights, are identified. Above 60,000 g-mol(-1), no surface enrichment could be detected; below 37,000 g-mol-1, the phase separation occurs with no dependence on the processing conditions; between these two limits, the phase separation depends on both, the formulation and the processing conditions. A correlation between the rheological measurements and the phase separation is given. A predictive criterion based on the viscous behavior of the blend is established. POLYM. ENG. SCI., 49:1177-1186, 2009. (C) 2009 Society of Plastics Engineers