Hello Ian,
Perhaps a mask would be of use here?
You mean: being able to pass a mask to the reduce function in Cactus?
Would be nice, unfortunately as far as I know, the "old" reduction interface using CCTK_Reduce (http://einsteintoolkit.org/usersguide/UsersGuidech9.html#verbatim-64) which Carpet uses does not let you pass in a param_table_handle the way that CCTK_ReduceGridArrays (http://einsteintoolkit.org/referencemanual/ReferenceManualch2.html#x4-165000...) does.
So one would first have to convert Carpet to support the "new" reduction interface (which is probably simple as the differences seem minor to me).
Yours, Roland