Irradiation of the heterostructure glass/Ta/Pt/GdFeCo/IrMn/Pt by 50 fs ultra-short laser pulses causes local thinning of the film down to ~12–30 nm depth. These pits are distinguished by Atomic Force Microscopy (AFM), while their stray magnetic fields were detected by Magnetic Force Microscopy (MFM). The crater was formed due to layer- by -layer evaporation of the material. No sign of melting was found in the vicinity of the crater at subthreshold laser fluence below 12–15 mJ/cm², but exceeding of the threshold caused destruction of the layers. Energy-dispersive X-ray spectroscopy (EDX) revealed depletion of Gd, Fe and Co, responsible for magnetic properties of the subthreshold crater. The amplitude of the local MOKE signal decreased down to 1.7 times in the irradiated area, while thinning of the ferromagnetic layer was 1.1 times. No proportional change of magnetization was caused by bias effect of IrMn layer. Decreased elastic modulus was found inside the subthreshold crater in the irradiated areas. Laser engineering of the surface of GdFeCo thin films opens the way for local control of energy balance between magnetic anisotropy, exchange coupling and Zeeman energy and creation of separated sectors for capture, storage and analysis of the ferromagnetic nanoparticles.