You should be able to use Dynamic modeler module’s Curve cut or Boundary cut tools to cut a surface with a curve that you draw on the surface. For this, you would need to copy your landmarks that are at the boundary into a new curve node as control points.
If you don’t want to construct a new curve then you can compute distance from your landmark points using vtkHausdorffDistancePointSetFilter then use vtkThreshold to extract the surface patch
You can also try to use Markups to model extension to convert your landmarks to a closed surface, use that closed surface with Surface to surface distance module, then finally extract the surface patch using vtkThreshold.
These require a few lines of Python scripting (get the polydata from a model node, run 1-2 VTK filters, and set the final result in a model node). There are examples in the script repository and you can ask here if you get stuck.