Hi Mark,
Simulink 3D Animation has also a MATLAB interface, you don't need Simulink in order to work with it. If you can describe the erosion as changing the shape of a planar border between pipe material and the inside medium, Simulink 3D Animation will be suitable. See the vrheat example how IndexedFaceSet objects (similar to MATLAB Patch objects) can be manipulated using SL3D MATLAB interface.
I can imagine applying also some plane fitting to best express the eroded shape by a simplified shape consisting of triangular / quadrilateral faces.
Best Regards,
Jan