The use of laser scanners in soft tissue microsurgery results in high quality ablations with minimal thermal damage to surrounding tissue. However, current scanner technologies for microsurgery are limited to free-beam lasers, requiring direct line-of-sight from outside the patient to the surgical site. Developing compact laser manipulation systems is crucial to introduce laser scanning capabilities in hard-toreach surgical sites. Recently, we developed a magnetic laser scanner as a tip module of an endoscopic system. The device provides 2D position control and fast scanning of a laser beam. In this work, the previous prototype is revised to enable its use with a CO2 laser source. The advantages of non-contact tissue ablations with fast scanning are discussed with comparative tissue ablation experiments coupling the system with a $CO_{2$ laser source. Results show that the magnetic laser scanner provides narrower ablations and less thermal damage compared to ablations performed with a bare flexible waveguide. These results highlight the potential of the proposed technology to improve soft tissue ablation quality in hard-to-reach surgical sites.