query about the capability of isosurface function

hello, suppose i have a 3D array containing data points, which i have generated by a algorithm, these data points corresponds to cross-sectional view of a complex objects (there may be many objects with in, they may be very close also). i want to color code each object differently and i need transparency. i am new to 3D visualization. can it handle intersection of two objects, if not can i write some code to do so. can i give some extra input to isosurface that will help it to know which points belong to which object. thanks