The morphology of an epitaxial layer defect has been studied in relation to the layer thickness and size/material type of a foreign particle on the starting substrate of a Si epitaxial wafer with (100) surface. As expected, the edge length of a square-shaped stacking fault or a crystal disorder on the (100) epitaxial surface becomes longer as the layer thickness increases. It is further revealed that the defect morphology is predominantly determined by the ratio of the substrate particle size, d, to the layer thickness, t. Micro-protrusion defects can appear when the ratio dir is relatively large. With decrease of the d/t ratio, the defect morphology gradually changes into a square-shaped stacking fault. The morphology dependence on the dir ratio is also influenced by the material type of the particle on the starting substrate wafer. The particle, which is deformable during epitaxial deposition, can generate a micro-protrusion when dir is large. However, this is not the case for an undeformable particle like a polystyrene microsphere. The defect morphology thus provides size and material characteristics information of a particle on the starting substrate wafer.