Select cells of a 3D model

Data = 3D volumetric brain Mesh
What would you like to do with the data? Need to select the surface cells from the brain portion where craniotomy was induced. I will be using the preoperative mri images.
What would you like to get as end results? after selecting cells I will save those cells in a file and will pass those cells along with the complete brain mesh to external Meshless algorithm to compute the craniotomy induced brain shift.