The spontaneous emission of fluorophores embedded in a photonic crystal has been studied. By nano-engineering a sandwich-like photonic structure, such that fluorophore-coated photonic atoms constitute a middle layer between the photonic crystals, we have been able to precisely control the location of fluorophores in photonic crystals and exclude the presence of fluorophores at the surface of the crystal. It has been found that the stopband in the transmission spectrum is deeper than the stopband in the emission spectrum. We conjecture that the omnidirectional propagation of the emission from a point source in an incomplete photonic bandgap is the cause of the shallower stopband in emission.