Using systematic atomistic modeling, the objective of this study is to explore the nanoscale tip-confinement effect in near-field surface nanostructuring. It is to provide important knowledge base for the understanding and design of tip-based manufacturing at the nanoscale.Our result reveals that the number of ablated-out atoms decreases significantly due to the tip-confinement. Tip apex oscillation occurs because of tip interaction with the substrate. The dynamic nanostructuring process and final surface structure are strongly affected by tip-substrate distance and laser fluence. When the tip-substrate distance is smaller, it takes a longer time for the substrate to cool down and solidify.