Lasers are a promising high accuracy tool to make small holes in composite or hard material. They offer advantages over the conventional machining process, which is time consuming and has scaling limitations. However, the major downfall in laser material processing is the relatively large heat affect zone or number of molten burrs it generates, even when using nanosecond lasers over high-cost ultrafast lasers. In this paper, we constructed a nanosecond laser processing system with a 532 nm wavelength laser source. In order to enhance precision and minimize the effect of heat generation with the laser drilling process, we investigated the geometric shape of optical elements and analyzed the images using the modulation transfer function (MTF) and encircled energy (EE) by using optical software Zemax. We discuss commercial spherical lenses, including plano-convex lenses, bi-convex lenses, plano-concave lenses, bi-concave lenses, best-form lenses, and meniscus lenses. Furthermore, we determined the best lens configuration by image evaluation, and then verified the results experimentally by carrying out the laser drilling process on multilayer flexible copper clad laminate (FCCL). The paper presents the drilling results obtained with different lens configurations and found the best configuration had a small heat affect zone and a clean edge along laser-drilled holes.