Well-ordered arrays of pits were prepared on gallium arsenide and silicon wafers using a finely focused ion beam (FFIB). The defect pits on gallium arsenide, examined with tapping mode scanning force microscopy (TM-SFM), had a rim diameter of 60 nm and were spaced 185 nm apart. TM-SFM images showed that human serum albumin (HSA) adsorption was highly specific to the inner portion of the rims of the pits on gallium arsenide, while there was no specific adsorption to the rims of pits on silica. This study demonstrates that a controlled spatial distribution of adsorbed proteins can be achieved on a nanometer scale and that the choice of material is of importance. Moreover, surface features such as pits and lines produced by FFIB can serve as a guide to easily reposition the TM-SFM probe tip at a specific location on the surface to within a few nanometers after temporary removal of the sample from the microscope.