Hiding individual cells from rendering and processing can be done using ghost arrays. Create a vtkUnsignedCharArray using vtkDataSet::AllocateCellGhostArray or vtkDataSet::AllocatePointGhostArray with the same number of tuples as the number of cells/points and set the individual values to vtkDataSetAttributes::HIDDENCELL or vtkDataSetAttributes::HIDDENPOINT. This array will serve as a binary mask effectively. See Ghost and Blanking (Visibility) Changes blog post for more details.