Heteroepitaxial diamond deposition on iridium substrates allows production of single crystal diamond layers on large area that is difficult to achieve with homoepitaxy. Critically important is the first stage of the process when diamond nucleates on Ir upon biasing (a voltage applied to the substrate). Here, we compared the heteroepitaxial nucleation and successive growth of diamond thin films in a microwave plasma CVD reactor on Ir/SrTiO3 substrates with different surfaces modified by bias voltage. The roughened surface consists of furrows and ridges while the flat surface is a little wrinkled. The film morphology, crystal quality and stress are characterized with SEM, AFM, TEM, X-ray diffraction and Raman spectroscopy. It is found that the film on the roughened Ir surface has a lower roughness, smaller mosaic spread, but a larger residual stress than the film deposited on the flat Ir surface, which mainly originates from the difference in the domain density. By comparing diamond (111) lattice spacings of different positions from the Ir-diamond interface, it is inferred that diamond nucleation could occur at the furrows and then overgrow the ridges for Ir-roughened sample while diamond may nucleate at the wrinkle and flat regions for Ir-flat sample. These finding are helpful in understanding of details of diamond film heteroepitaxy, and in searching the ways to improve their crystallinity.