We report an improved method for production of microfluidic device masters using two-photon photopolymerization of SU-8 negative photoresist, which relies on a two-photon microscope (TPM) commonly used in imaging of biological samples. The device masters serve as negative relief structures for polydimethylsiloxane-based microfluidic devices. We observed that not only did the two-photon excitation of the SU-8 photoresist initiate crosslinking of the material in the region of the focus of the near-infrared laser beam (as expected) but it also resulted in emission of fluorescence in the visible range. The detected emission of SU-8 photoresist undergoing two-photon excitation displayed a strong correlation with the size of the polymerized objects produced during the exposure; this allowed the progress of the microfluidic master production process to be monitored in real-time. We demonstrate the use of the fluorescence detection during two-photon photopolymerization in the production of microfluidic devices, which were designed to trap individual yeast cells to be imaged with the same TPM used for microfluidic master writing.