Interface magnetism and topological structure of Fe on organic semiconductor film (Alq3) have been studied and compared with Fe film deposited directly on Si (100) substrate. To get information on the diffused Fe layer at the Fe/Alq3 interface, grazing incident nuclear resonance scattering (GINRS) measurements are made depth selective by introducing a 95% enriched thin 57Fe layer at the Interface and producing x-ray standing wave within the layered structure. Compared with Fe growth on Si substrate, where film exhibits a hyperfine field value of 32 T (Bulk Fe), a thick Fe- Alq3 interface has been found with reduced electron density and hyperfine fields providing evidence of deep penetration of Fe atoms into Alq3 film. Due to the soft nature of Alq3, Fe moments relax in the film plane. At the same time, Fe on Si has a resultant ~43 deg out-of-plane orientation of Fe moments at the Interface due to the stressed and rough Fe layer near Si. The evolution of magnetism at the Fe-Alq3 Interface is monitored using in-situ magneto-optical Kerr effect (MOKE) during the growth of Fe on the Alq3 surface and small-angle x-ray scattering (SAXS) measurements. It is found that the Fe atom tries to organize into clusters to minimize their surface/interface energy. The origin of the 2.4 nm thick magnetic dead layer at the Interface is attributed to the small Fe clusters of paramagnetic or superparamagnetic nature. The present work provides an understanding of interfacial magnetism at metal-organic interfaces and the topological study using the GI-NRS technique, which is made depth selective to probe magnetism of the diffused ferromagnetic layer, which is otherwise difficult for lab-based techniques.