The preparation of small-sized biological samples is traditionally performed manually utilizing mechanical tools such as scalpels. The main drawbacks of such methods are a lack of accuracy and repeatability of the resulting cuts and damage to the surrounding tissue due to the high interaction forces and the accompanying mechanical stresses. One way to circumvent these issues is to substitute the mechanical tools for laser light. When used in conjunction with a high-accuracy positioning system, such a preparation procedure enables repeatable cutting of arbitrary geometries while largely preserving the integrity of the surrounding tissue. In this paper, a system leveraging the potential of laser-based ablation for bio-sample preparation is proposed. It integrates and synchronizes all key components with extensive safety features and an intuitive user interface, allowing novice operators to perform sample preparations easily. As a first application, the proposed system has been utilized to create microdamages in mouse tail tendon fascicles. Promising results could be obtained, but careful tuning of the laser parameters and further optimization of the mechanical setup is still required to attain the high repeatability striven for.