The defect structure, the degree of crystalline perfection and the surface roughness of HTc superconductor films are affected by the initial layer configuration at the early stage of growth. In this work we report on structural and morphological investigations of ultrathin YBa2Cu3O7-x films grown on SrTiO3 substrate, The films are fabricated by inverted cylindrical magnetron sputtering with a modified deposition process based on the modulation of sputtering power. The modulated sputtering deposition promotes a higher in-plane grain connectivity and allows us to fabricate films with a lower defect density. The structural analyses of very thin films (thickness <25 nm) are performed by using low-angle x-ray specular reflectivity, double crystal diffraction, reciprocal space mapping and atomic force microscopy. The results indicate that a total relaxation of our films occurs at layer thickness larger than 25 nm. For thinner layers a tetragonal distortion of the unit cell and no twinning are observed. The low-angle measurements show distinct Kiessig fringes revealing a smooth surface and film/substrate interface. The off-specular reflectivity measurements indicate that the surface and interface roughness across the YBa2Cu3O7-x layer are uncorrelated.