The effect of simple in situ vacuum treatment between the sequentially multilayered YBCO thin films by pulsed laser deposition is investigated. The vacuum treatment during the growth intervals is observed to have a diminishing effect on the formation of structural defects along the c-axis of the YBCO lattice. This greatly improves the structural properties of the film, ultimately resulting in almost 40% increased self-field critical current density. The underlying mechanisms behind the vacuum treatment are comprehensively discussed with the help of Kinetic Monte Carlo simulations, suggesting that the improved crystalline quality of each sublayer results from desorption of weakly bound atomic species from the film surface thus reducing probability of defect formation in the following ablation interval.