In order to detect samples with convenience, high speed and low cost, we presented a fabrication method of microchip with embedded optical fibers. Polymethyl methacrylate (PMMA) microchip with embedded optical fibers of 35 μm diameter was fabricated using a 248 nm KrF excimer laser processing technique. The processing parameters of excimer laser and the embedding method of optical fibers were studied. The results show that the excimer laser processing is controllable, easy, reliable to realize automation. With the embedded optical fiber system, the mutual aim of the fibers and the aim between the fibers and channel core can be realized, thus resulting in the sensitive detection of optical signal, which is expected to have good applications in the portable blood cell counts and bio-sensors.