Depends on the amount of interference you have, which can vary due to manufacturing tolerances and core shift in the head casting... the exhaust manifolds aren't really all that thick, and like I said the heads have a coolant passage right below the surface in that area. Test fit it, and eyeball it to determine the amount of clearance needed, and make your choice as to how you want to handle it.
Remember, this is only with the '64-'66 manifold.
With Magnum heads, in the instance I showed above, it looks like a bit of cleanup grinding on the casting flash on the lower part of the head (the interference is in a totally different area) may gain you enough clearance. Again, test fit the manifold and make your choice.
In both instances you are trying to marry parts that were not designed to go together, so some concessions and modifications will be necessary- the extent of which will need to be determined in your own circumstance. I prefer to err on the side of caution.