The surface structure of an individual metal-organic framework (MOF) microcrystal grown on a functionalized surface has been successfully investigated for the first time in air and vacuum using high-resolution atomic force microscopy. Moreover, this detailed surface analysis has been utilized to optimize the MOF formation procedure to obtain a defect-free surface structure. Comparison of obtained data with recent microscopic studies performed on the same MOF crystal but grown by a conventional procedure clearly shows a much higher quality of crystals produced by surface oriented growth. Importantly, this method of preparing crystals suitable for microscopic analysis is also much faster (3 days compared to 2 years) and, in contrast to the conventional method, produces material suitable for in situ study. These results thus demonstrate for the first time the possibility of nanoscale investigation/modification of MOF surface structure.