The spatial resolution plays a crucial role in determining the performance of a nuclear microprobe. However, the formation of spatial resolutions below 10 nm remains a challenge in nuclear microprobes. Here, we propose novel technologies (near-axis scanning transmission ion microscopy and double-fragment scattering) utilizing molecular ions to address this challenge and demonstrate a H2+ molecular beam with 6.0 × 10 nm2 lateral resolution and monolayer thickness resolution respectively. Using the improved nuclear microprobe, we directly demonstrate that the ionization of a H2+ can be efficiently achieved using one single layer graphene, and also that single and few layers of freestanding graphene can be clearly differentiated and identified. The precise control of fast molecular ions at sub-10 nm scales has the potential to unlock new avenues of applications.