Create sub-surfaces from a 3D-surface

Hi all,
I have a 3D-surface and the coordinates of different boundaries on this surface. From these data I would like to create sub-surfaces from which computing the centroid. Right now, I was able to compute the centroid considering only the boundary points, but, of course, these points do not always belong to the surface.
Thank you

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Pictorial example will help.
As you can see, the blu/light blu mesh is the whole surface, and the red boundary outlines the sub-surface I want to work with.
Okay..as you have the boundary points for the sub surface (red curve) you can pick the points lying inside that surface right?
I don't know how to do it, it's what I'm trying to achieve, because the two meshes (whole and boundary) are from two different files.
Thank you! To be honest I don't think this is going to help me though, but I'll try.
Have a look here as well: https://www.mathworks.com/matlabcentral/answers/101396-is-there-a-function-in-matlab-for-detecting-points-inside-a-polyhedron

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