Combined scanning tunneling microscopy, spectroscopy and local barrier height (LBH) studies show that low-temperature-cleaved optimally-doped Ba(Fe1-xCox)2As2 crystals with x=0.06, with Tc = 22 K, have complicated morphologies. Although the cleavage surface and hence the morphologies are variable, the superconducting gap maps show the same gap widths and nanometer size inhomogeneities irrelevant to the morphology. Based on the spectroscopy and LBH maps, the bright patches and dark stripes in the morphologies are identified as Ba and As dominated surface terminations, respectively. Magnetic impurities, possibly due to cobalt or Fe atoms, are believed to create local in-gap state and in addition suppress the superconducting coherence peaks. This study will clarify the confusion on the cleavage surface terminations of the Fe-based superconductors, and its relation with the electronic structures. ; Comment: Accepted to Nano Letters (5 figures)