Ultra-precision slow tool servo (STS) machining can directly generate high-precision continuous and discontinuous freeform surfaces. However, in the fabrication of a micro-lens array (MLA) by STS, a single lens achieves different levels of quality. In addition, the low quality of a single lens may induce the failure of the entire functional component. To study the factors affecting the machining precision of an MLA on a spherical surface in STS, an experimental investigation was conducted. Specifically, the effects of the geometries of the base surface and position of a single lens on the machining precision of an MLA were examined. In the experiments, an MLA was machined by STS into three spherical surfaces having different radii, and Bruker GT-X was used to measure the base surface and micro lenses. The effects of the base surface and lens positions on the surface roughness and form error of a single lens were studied. Experimental results show that the position of the single lens changes the surface topography, surface roughness, and form accuracy of the lenses on the same base surface. In addition, the geometrical information of the base surface changes the machining precision. When the radii of base surfaces are increased from 50 to 150 mm, the surface roughness of the outer circle lens decreases from 75.78 to 69.08 nm (Ra). Therefore, considering the effect of the base surface and lens position on machining precision in the ultra-precision STS machining of MLAs is necessary. This may contribute to improving the precision consistency of MLAs and ensuring proper component function.