The morphology and periodicity of arrays of single focused-ion-beam induced artificial defects in graphite is probed using scanning tunneling microscopy and modeled through Monte Carlo simulation. While ion dose is kept constant with a fluence of 2.48 x 10(15) ions cm(-2), variations in artificial defect morphology are attributed to astigmatism in the beam aperture, to deviation in beam angle, or to distance from beam focal point. Simulation of the collision cascade of the ion in graphite lattice correlates to the artificial defect dimensions of both circular symmetric and elongated asymmetric defects. Periodic arrays of artificial defects exhibit constant periodicities at lower basis dimensions (100 nm separation between defects), with larger deviations from the periodic structure at higher basis dimensions (400 nm separation between defects). Well structured periodic arrays of defects are considered for nanostructured patterning of molecules for thin film growth. Local amorphization of graphite due to ion irradiation changes the diffusion field, which can be tailored for the guided self-assembly of molecules. (C) 2009 American Vacuum Society. [DOI: 10.1116/1.3212935]