1. A method of making a bonded intermediate substrate, comprising: forming a weak interface in a GaN source substrate by implanting ions into an N-terminated surface of the GaN source substrate; bonding the N-terminated surface of the GaN source substrate to a handle substrate; exfoliating a thin GaN single crystal layer from the source substrate such that the thin GaN exfoliated single crystal layer remains bonded to the handle substrate and a Ga-terminated surface of the thin GaN single crystal layer is exposed; depositing a capping layer directly onto the exposed surface of the thin GaN single crystal layer; and annealing the thin GaN single crystal layer in a nitrogen containing atmosphere after depositing the capping layer, wherein an in-plane strain present in the thin GaN single crystal layer after the annealing is reduced relative to an in-plane strain present in said layer prior to the annealing.