We perform detailed radiative transfer modeling of the emission expected from magnetic flares in Active Galactic Nuclei (AGN). We assume a compact flare source above the accretion disk surrounding a supermassive black hole. The source is supposed to be anchored in the disk by magnetic structures and orbits around the center on Keplerian time scales. For the spectral modeling we take into account the primary radiation coming directly from the flare source and a Compton reflection/reprocessed component coming from the disk surface. The disk is supposed to be in hydrostatic equilibrium. Its density, temperature and ionization profiles are computed self-consistently. We take into account the variations of the incident radiation across the hot-s...