Femtosecond laser surface processing (FLSP) is an emerging technique for creating functionalized surfaces with specialized properties, such as broadband optical absorption or superhydrophobicity/superhydrophilicity. It has been demonstrated in the past that FLSP can be used to form two distinct classes of mound-like, self-organized micro/nanostructures on the surfaces of various metals. Here, the formation mechanisms of below surface growth (BSG) and above surface growth (ASG) mounds on polycrystalline Ni60Nb40 are studied. Cross-sectional imaging of these mounds by focused ion beam milling and subsequent scanning electron microscopy revealed evidence of the unique formation processes for each class of microstructure. BSG-mound formation during FLSP did not alter the microstructure of the base material, indicating preferential valley ablation as the primary formation mechanism. For ASG-mounds, the microstructure at the peaks of the mounds was clearly different from the base material. Transmission electron microscopy revealed that hydrodynamic melting of the surface occurred during FLSP under ASG-mound forming conditions. Thus, there is a clear difference in the formation mechanisms of ASG- and BSG-mounds during FLSP.