A couple of things:
1. If size(MM(looper,:),1) is independent of looper (as you suggest?), you can simply precalculate it before the loops.
2. Depending on your specific data cell2mat(C(looper,looper2)) can be vectorized by precalculating C2=cell2mat(C); be careful with indexing afterwards though (because all will be merged in one large array). Much easier, if C(looper,looper2) all have the same dimension is to get rid of cells altogether and store your C data in higher dimension matrices.
3. Test for ~isnan(currPoint(1)) before calling distancePoints3d, since if it is NaN the output of distancePoints3d is not used.
4. If you have managed to speed up the code, please post the new code, so we can work on the remainder :)