a b s t r a c t a r t i c l e i n f oTo assess diamond-based semiconducting devices, a reduction of point defect levels and an accurate control of doping are required as well as the control of layer thickness. Among the analyses required to improve such parameters, cross sectional studies should take importance in the near future. The present contribution shows how FIB (focused ion beam) preparations followed by electron microscopy related techniques as TEM or CL allowed to perform analysis versus depth in the layer, doping and point defect levels. Three samples grown along the same week in the same machine with identical growth conditions but on different substrates (CVD-IIIa (110) oriented, CVD-optical grade (100) oriented and a HPHT-Ib (100) oriented) are studied. Even though A-band is observed by CL, no dislocation is observed by CTEM. Point defect type and level are shown to substantially change with respect to the substrate type as well as the boron doping levels that vary within an order of magnitude. H3 present in the epilayer grown on HPHT type of substrate is replaced by T1 and NE3 point defects for epilayers grown on the CVD type one. An increase of excitonic transitions through LO phonons is also shown to take place near the surface while only TO ones are detected deeper in the epilayer. Such results highlight the importance of choosing the correct substrate.