A series of enzymatic degradation experiments were designed to examine the surface morphology of phase separated poly(ε-caprolactone) (PCL)/poly(ethylene oxide) (PEO) blend films. Candida antarctica Lipase B (CALB), previously reported to have superior degradation selectivity when used at low concentrations, was utilized to selectively dissect interlamellar amorphous PCL chains and therefore to reveal the crystalline region of PCL phase. Water soluble PEO can be simultaneously removed by the CALB aqueous solutions, allowing one to envision the topological features of phase separated PCL/PEO films with various blend ratios. The transition of phase-separated PCL/PEO from nucleation and growth to spinodal decomposition was fully mapped out, along with the spatial distribution and surface morphological features of the crystalline PCL phase. The morphological characteristics of PCL/PEO blend films were further correlated to their reported physicochemical properties, demonstrating the impact of microscopic structures on the macroscopic properties of given semicrystalline polymer systems.