Nanostructured BaTiO3 polar thin films are increasingly critical to the function of future multilayer ceramic capacitors and related oxide-based electronic devices. The effect of surface charges on BaTiO3 polarization behavior is therefore investigated by ultra-high vacuum scanning probe microscopy (UHV-SPM) for 3 distinct morphologiesepitaxial, polycrystalline, and nanocrystalline films. Regardless of the film morphology, Kelvin probe force microscopy reveals that BaTiO3 thin film surfaces exhibit positive charging after contact scanning by various noble AFM probes due to the work function difference between tip and specimen. According to piezoresponse force microscopy, these positive charges uniformly stabilize downward polarized domains. However, the hysteresis and concomitant surface charging behavior are strongly sensitive to microstructure and defects. In particular, the stability and switching behavior are influenced by bulk and interfacial defect distributions and hence correlated to film deposition methods and grain size. Such morphology dependent properties for BaTiO3 films are revealed only through UHV measurements where screening charges from the ambient can be minimized, demonstrating the importance of UHV-SPM for understanding ferroelectric thin films and nanostructures.