The aim of this work is to study the influence of (100) substrate pre-treatment before boron doped homoepitaxial diamond growth. Atomic force microscopy measurements were made on (100) Ib HPHT and (100) IIa chemical vapour deposition commercially available substrates after the classical acid cleaning and before any growth or treatment. The (100) Ib HPHT substrates exhibit the most reproducible surfaces (on both sides). Different treatments before growth were performed on this type of substrates (hydrogen plasma etching, ion implantation, etc.). We show that a combined ion implantation and H2 plasma etching pre-treatment improves drastically the substrate roughness, with values as low as 0.2 nm readily obtained.