Optimal design and fabrication of novel devices for high-performance optofluidic applications is a key issue for the development of advanced Lab-on-a-Chip systems. Parallel cell counting with a high success rate and simple mode of operation is a challenging goal. Current cell-counting methods, using optical waveguides or flow cytometry, typically require a precise coupling of the probe light and involve complex operations. In the present paper, a novel multifunctional cell counting microdevice is designed. It uses a center-pass optofluidic microlens array (MLA) consisting of seven microlenses and an M-shaped confining wall with 9-m-diameter apertures. The device can be fabricated in a three-dimensional microchannel by ship-in-a-bottle femtosecond laser integration based on two-photon polymerization with optimized experimental parameters. Each microlens produces approximately the same intensity at the focal positions (within ±5%) under white-light illumination, while the 6- to 8-m-wide confining wall restricts cells to passing through the edges of two adjacent microlenses because the aperture opens toward their centers. The device demonstrates coupling-free parallel cell counting with a 100% success rate by monitoring the optical intensity variations at each spot. As a result, this method features both easy operation and high performance. Furthermore, the confining wall can filter deformed cells having 15-m width. Keywords: 3D optofluidic chip, two-photon polymerization, microlens array, cell counting, ship-in-a-bottle integration.