For the first time, focused ion beam milling, secondary electron microscopy, and transmission electron microscopy were used to examine in depth morphological defects during epitaxial growth of CdTe and CdSeTe on Si. Contrary to the literature regarding the formation of morphological defects at the epi/ substrate interface, the present defects appear to originate from either the CdTe/CdSeTe interface or 3-4 µm above the CdTe/Si interface where the growth was interrupted and the substrate temperature was temporarily raised. This suggests a correlation between defect nucleation and either shutter movement or growth interruption.