Large areas of regular diffraction nanogratings were produced consisting of so-called laser-induced periodic surface structures (LIPSS) on thin molybdenum layers (<400 nm ) deposited on a borosilicate glass substrate. The aim was to produce these structures without ablating nor cracking the molybdenum layer. Ultra short laser pulses were applied using a focused Gaussian beam profile. Processing parameters such as laser fluence, pulse overlap, number of overscans, repetition frequency, wavelength and polarization were varied to study the effect on periodicity, height, and especially regularity of the obtained LIPSS. It was found that a careful choice of the correct laser parameters is required to avoid detrimental mechanical stresses, cracking, and delamination during the laser processing of the layer in order to remain in its correct range of ductility as well as to ensure regular LIPSS. A possible photovoltaic application of these nanogratings could be found in texturing of thin film cells to enhance light trapping mechanisms.