Two issues relating to the determination of junction position in thin film CdTe solar cells have been investigated. Firstly, the use of a focussed ion beam (FIB) milling as a method of sample preparation for electron beam induced current (EBIC) analysis is demonstrated. It is superior to fracturing methods. High quality secondary electron and combined secondary electron/EBIC images are presented and interpreted for solar cells with CdTe layers deposited by both close space sublimation (CSS) or RF sputtering. Secondly, it was shown that in an RF-sputtered CdTe device, while the photovoltaic junction was buried ~1.1 μm from the metallurgical interface, the shape of the external quantum efficiency (EQE) curve did not indicate the presence of a buried homo-junction. SCAPS modelling was used to verify that EQE curve shapes are not sensitive to junctions buried < 1.5μm from the CdTe/CdS interface.