We study the effects of feedback from active galactic nuclei (AGN) on emission from molecular gas in galaxy mergers by combining hydrodynamic simulations which include black holes with a three-dimensional, non-local thermodynamic equilibrium (LTE) radiative transfer code. We find that molecular clouds entrained in AGN winds produce an extended CO morphology with significant off-nuclear emission, which may be detectable via contour mapping. Furthermore, kinematic signatures of these molecular outflows are visible in emission line profiles when the outflow has a large line of sight velocity. Our results can help interpret current and upcoming observations of luminous infrared galaxies, as well as provide a detailed test of subresolution prescriptions for supermassive black hole growth in galaxy-scale hydrodynamic simulations.