A modification on a laser scanning ablation system capable of preparing large area YBa2Cu3O7 (YBCO) thin films has been made. With this modification, YBCO films with various thicknesses can be deposited in-situ on several pieces of substrates under essentially identical deposition conditions, and particularly, in a continuous fashion. Films of sequential thickness on different substrates were then studied by atomic force microscopy to investigate the effects of lattice mismatch and treatments of substrate on the growth mechanism of YBCO films.