Can use an image or a DXF file to group 3D data points according to areas in the image and store the data for further analysis?

I have an H5 file with position and voltage data collected from meshpoints on a 2D model. When the h5 file is created, it losses information about the original domains (areas) of the model (which has a DXF file format) and it only has the meshpoints. The model is of a spinal cord so you can think of it as concentric shapes. I would like to group the different voltages with their associated domain (gray matter, white matter, etc.)and analyze the data from the mesh points separately. My approach was to overlay the original model on the 3D data plot and somehow use the outlines to tell Matlab which points to include, but I am not sure how I can do this. Is there some way to do this? Does anyone have a better approach to how I can group the points together and have the data+ position in one matrix for each of the domains? Can I apply the solution to an extruded 3D model (it would have a Parasoild (.x_b) format). Please let me know if my problem is still unclear.