This paper reports the tunability of magnetic domains and its correlation with depth-resolved microstructure in 100 nm thick Gd-Fe films after rapid thermal processing. The as-deposited films are amorphous in nature and display elongated periodic stripe domains, signifying the development of perpendicular magnetic anisotropy. Rapid thermal processing at 550oC for different time intervals viz. 5, 10, 15 and 20 min induces the crystallization of Fe over the amorphous Gd-Fe matrix and the presence of wider reaction zone has been evidenced at the film-substrate interface. While the magnetization measurements reveal a spin re-orientation along the plane of the film surface, the stripe domains are no longer observed for the processed films. 3D micromagnetic simulations have been performed to complement the experimental findings. The consideration of in-plane tilt of anisotropy axis along with anisotropy reduction successfully demonstrate the experimentally observed changes in magnetic properties and domain structure. © 2018 Elsevier B.V.