In this paper, we present a micro-electro-mechanical-system based on a microcapillary electrophoresis chip device integrated with optical detection components, including a micro-focusing lens structure and buried optic fibers. This is a promising approach to enhance the optical signal of the laser-induced fluorescence system for biomedical detection applications. This study utilized microcapillary electrophoresis (micro-CE) chips with two specific polymer materials, polymethylmethacrylate (PMMA) and polydimethylsiloxane (PDMS). Both are capable of performing multiple-wavelength fluorescence detection by using integrated optic components. These include multimode optic fiber pairs and a micro-focusing-lens structure, embedded downstream of the separation channel. For detection purposes, the fluorescence signals are enhanced by positioning micro-focusing-lens structures at the outlets of the excitation fibers and the inlets of the detection fibers. In this study, two types of micro-focusing-lens are proposed—fixed-focal-length and controllable micro-lenses. They are made from different materials—PMMA and PDMS, respectively. With regard to the fixed-focal-length micro-lenses, the profile of the micro-lens curve can be formed by the defined master mold with specific temperatures and pressures. With regard to the controllable micro-lens design, deformations of the two flexible surfaces can be generated after pressurized index-matching fluid is injected into the pneumatic side-chambers. The side-chambers can be deflected as a double convex lens to focus both the excitation light source and the fluorescent emission signal. Experimental results revealed that the power amplitude of the excitation laser light can be enhanced by up to 5.4 fold. Fluorescein isothiocyanate, dye labeled protein samples and DNA markers are then utilized for micro-CE chip testing. The results indicated that signal amplitude can be enhanced from 1.7 to 2.6 fold when compared with cases without the micro-lens. According to the experimental results, the developed device has a great potential to be integrated with other microfluidic devices for further biomedical applications.