When defining component clearance in Altium it warns you when 2 components are too close, but, it also warns you even when the components are on different layers so obviously they can't collide.
As described here you can use Multi Layer Check for collision checking:
But in Altium 14.1 I don't see this option:
Where is this option located now? I can't find it anywhere! I even tried using Query to try to get this behavior but it didn't work.
Here for example I get a warning between Multi-Layer and Top Overlay on the same component!
Best Answer
I haven't gotten really familiar with AD 14 yet, but you could just write two rules, Top_Clearance and Bottom_Clearance.
Top clearance has Where The First Object Matches: Layer Top
Where The Second Object Matches: Layer Top
Bottom_Clearance is similar. Although I've never seen a clearance check problem between two LAYERS. If I remember correctly, this is how AD 10 works too. Maybe you need to define some more accurate/realistic 3D bodies? Or maybe I don't fully understand your problem.