In order to better simulate heat fluxes over multilayer ecosystems, in particular tropical forests and savannahs, the next generation of Earth system models will likely include vertically-resolved vegetation structure and multi-level energy budgets. We present here a multi-level radiation transfer scheme which is capable of being used in conjunction with such methods. It is based on a previously established scheme which encapsulates the three dimensional nature of canopies, through the use of a domain-averaged structure factor, referred to here as the effective leaf area index. The fluxes are tracked throughout the canopy in an iterative fashion until they escape into the atmosphere or are absorbed by the canopy or soil; this approach explicitly includes multiple scattering between the canopy layers. A series of tests show that the results from the two-layer case are in acceptable agreement with those from the single layer, although the computational cost is necessarily increased due to the iterations. The ten-layer case is less precise, but still provides results to within an acceptable range. This new approach allows for the calculation of radiation transfer in vertically resolved vegetation canopies simulated in global circulation models.