The advanced application of magnetoelectric cantilver sensors for biomagnetic sensing puts huge emphasis on the material engineering of the magnetostrictive phase. With this regard, ultra-thin films of FeCo alloy have been magnetically decoupled by layers of TiN to ensure high thermal stability, large magnetostriction and soft magnetic hysteresis loops, which coercive field scales with the individual FeCo layer thickness. With respect to the FeCo layer thickness, we investigated three samples restricting the FeCo layer to 3 and 5 unit cells and having a bilayer thickness of Λ = 3.3, 4.7 and 7.3 nm, respectively. Dedicated methods of transmission electron microscopy (TEM), such as aberration-corrected scanning TEM, and X-ray diffraction (XRD) reveal a complex microstructure of rotationally aligned columns with individual, atomic flat layers grown pseudomorphic to compensate for the lattice mismatch. However, this introduces an in-plane strain component resulting in a tetragonal distorted FeCo lattice creating uniaxial magnetic anisotropy contributions which puts large constraints on the envisioned magnetic properties as demonstrated by high-resolution microscopy on the atomic scale. Further, we compare the structural and chemical information obtained from X-ray reflectivity and high-resolution TEM measurements on specimen tempered by ex situ and in situ approaches with respect to evolution of strain and thermal stability.