A couple of relevant tools:
- Baffle Planner: define open surface using boundary curve and surface points
- Dynamic modeler module (in recent Slicer Preview Releases): cut out arbitrary piece from a mesh using cutting plane(s) or a rectangular ROI
- Resect objects using warped plane (in LiverAnalysis extension): Unfortunately, this extension has not been submitted to the extension manager yet and therefore you need to build it. @RafaelPalomar is there a reason why this extension has not been submitted to the extension manager?