Femtosecond laser surface processing (FLSP) can be used to functionalize many surfaces, imparting specialized properties such as increased broadband optical absorption or super-hydrophobicity/-hydrophilicity. In this study, the subsurface microstructure of a series of mound-like FLSP structures formed on commercially pure titanium using five combinations of laser fluence and cumulative pulse counts was studied. Using a dual beam Scanning Electron Microscope with a Focused Ion Beam, the subsurface microstructure for each FLSP structure type was revealed by cross-sectioning. The microstructure of the mounds formed using the lowest fluence value consists of the original Ti grains. This is evidence that preferential laser ablation is the primary formation mechanism. However, the underlying microstructure of mounds produced using higher fluence values was composed of a distinct smaller-grained α-Ti region adjacent to the original larger Ti grains remaining deeper beneath the surface. This layer was attributed to resolidification of molten Ti from the hydrodynamic Marangoni effect driven fluid flow of molten Ti, which is the result of the femtosecond pulse interaction with the material.