We report a novel methodology for fabricating a sub-micron spherical atomic force microscope (AFM) tip controllably - a silicon sub-micron sphere atop microcantilevers, which is desired for precise nanoscale tribology measurements, biological studies, and colloid science. Silicon sub-micron spheres are fabricated through swelling of single-crystal silicon with proper high-energy helium ion dosing, a traditionally undesired phenomenon known in helium ion microscopy. Silicon sub-micron spheres with diameters from 100 nm to 1 μm are demonstrated, and the placement of silicon sub-micron spheres can be as accurate as 10 nm or even below. This AFM tip demonstrates robust measurements during friction tests on graphene/silicon oxide substrates for more than 10 »000 cycles. This AFM tip overcomes a critical challenge of reducing the size of spherical AFM tips from the micrometer scale to the sub-micron scale and is promising in cross-scale mechanics studies, nanotribology, colloid science, and biology.