We proposed the low energy ion irradiation effects (ion excitation and ion etching) on the formation and the top-surface properties of sp(2) nanocrystallited carbon films in electron cyclotron resonance (ECR) plasma sputtering system. In this work, the ion etching rate during film deposition was measured and a threshold voltage for physical etching was found to be about 35 V. Below the threshold voltage, the film growth was induced by ion excitation effect (ion exciting electrons of top-most atoms), as a result, the sp(2) dominant nanocrystallite size in the films was large. When the ion energy exceeded the threshold voltage, the film growth was induced by ion etching effect (ion breaking covalent bond), and the nanocrystallite size was small confirmed by the transmission electron microscopy (TEM) observation and Raman analysis. Furthermore, the top-surface properties of sp(2) nanocrystallite carbon films prepared with different ion irradiation effects were examined by using the atomic force microscopy (AFM). Results showed that the ion etched carbon films had smaller surface roughness, scratch depth and adhesive force compared with the ion excited carbon films. These findings shed light on the fabrication and applications of carbon based nanostructured materials.