Microlens arrays are widely used as critical components in a large number of photonics and telecommunication products. The increasing demand for high-tech products provides an expanding room for the development of the micro-fabrication technology. This study presents a tool compensation for correcting the form error of fabricated microlenses in ultra-precision machining with fast-tool-servo (FTS) system. After presentation of optimal cutting conditions deduced on the basis of cutting experiments of microlens arrays, a tool radius compensation method will be proposed and evaluated in this paper. This methodology makes use of form measurement data from a Form Talysurf system to modify the C program employed in the software of ultra-precision machining FTS system – SOP. The form error was successfully reduced after implementation of tool compensation.