In this work, a detailed report on the growth of elongated bar-like crystallites with a definite crystallographic orientation, forming a self-organized patterned surface layer, with a thickness of about 100 nm, onto 900 nm thick ferromagnetic shape memory alloy Ni-Mn-Ga films epitaxially grown on MgO(001) is presented. The phenomenon appears above a threshold of lattice mismatch (≈2%) between the film and substrate. The structural, magnetic and transformation properties of such films are described and analyzed. Particularly, the different magnetic states of the two film layers are discerned by ferromagnetic resonance. The feasibility of creating a ferromagnetic shape memory alloy with a nanoscale self-patterned surface, during the very same process of film deposition, can be interesting for potential applications where control of the surface architecture would be needed.