For example along the Z-axis? i have a model essentially consisting of multiple UV sphere’s that intersect one on top of the other, if you must know it’s a Weedle , as in the Pokemon. 
So i don’t know if it really matters but the only way i could think to clean up the intersecting bit’s was to delete the top vertex’ and merge them with the bottom of the above sphere.
I don’t really fancy always doing it one point at a time because for every sphere it would take aaaages, so if i can select all the vertex’ and merge them with the ones above them , thus connecting the two spheres i would prefer it. If what i ask isn’t possible , what would you suggest doing? and does it even matter? i plan on rigging it to pose it slightly too.
Thanks!