The new Si epitaxial (epi) defects not seen in scanning electron microscope (SEM) measurements were investigated. Morphologies of these defects were measured by atomic force microscope (AFM) but source of defect was not found in transmission electron microscope (TEM) measurements. In order to find the origin of the invisible defect, we observed the morphological changes of the various substrate defects after epi growth process. Most of the defects were removed during hydrogen (H-2) baking and hydrogen chloride (HCl) etching steps, but some particles survived. Among the survived defects, it was confirmed that the non-metallic particles having 200 nm or more were the origin of the invisible epi defects.