We present the surface microfabrication of CYTOP, an amorphous UV transparent fluoric polymer, using a conventional pulsed green laser. Fluorine-based polymers have unique characteristics, including high transparency from the deep-UV to the IR wavelengths, chemical stability and low refractive indices, and thus are expected to have a number of industrial applications. However, CYTOP and other fluoric polymers are generally very difficult to microfabricate unless to use high particle beams. Therefore, we have developed a technique for the crack-free surface microfabrication of a CYTOP substrate based on ablation with a pulsed green laser followed by successive wet etching and annealing. In this work, the fundamental surface characteristics of the fabricated area were investigated. After the surface microfabrication of CYTOP, a three dimensional biochip was fabricated using a conventional PDMS bonding technique to demonstrate that a CYTOP biochip is superior to conventional transparent biochips with regard to the microscopic observation of cell motion.