Ultrashort pulsed lasers are being increasingly used for high precision micromachining across many industries. To further optimise these processes, consideration of the spatial profile of the laser beam is essential, as the shape of the processed area often closely resembles the intensity distribution used. Within surgical contexts, ultrashort infrared pulsed lasers offer significantly improved localisation in the ablation of biological tissues over current electrocautery methods through their non-contact, plasma-mediated interaction mechanisms. This localisation can reduce the risk of severe complications such as bowel perforation. However, for incorporation into an endoscopic device, the limited focal depths inherent to tightly focused Gaussian beams can greatly hinder the ablation of inhomogeneous tissue surfaces. However, alternative beam shapes, such as Bessel-Gauss beams, enable a decoupling of the focal volume from the focal depth. Various beam profiles and laser scanning parameters have been investigated, capitalising upon the distinct advantages offered from applying ultrashort pulsed lasers to microsurgery of tissue. Assessment of the corresponding ablation profiles in porcine intestinal tissue was performed through both three-dimensional optical surface profilometry and histological analysis. Using a Bessel-Gauss beam, ablated depths close to a millimetre were achieved while showcasing peak thermal damage margins of around 30 μm. If adopted in operating theatres, surgeons could benefit from increased precision when resecting neoplasia in the mucosal and submucosal layers of the colon, providing them with greater levels of control both in terms of lateral accuracy and in moderating the depth of tissue removed, especially when compared to current electrocautery methods.