By comparing finite-difference time-domain near field simulations and femtosecond laser ablation of thin films, we characterize in three dimensional-space photonic nanojets from microsphere arrays. We demonstrate periodic drilling of transparent films with thickness up to 100 nm (onto absorbing substrates) is feasible with 1-microm diameter silica spheres. Working with larger polystyrene spheres, the apparent increase of the propagation length of the photonic nanojets makes possible to drill films as thick as 500 nm. Interestingly, the lateral width of the produced craters can be maintained below 400 nm evidencing the low divergence of the nanojets. For backside illumination of the arrays, the ablation features are located at the top of the microspheres. We reveal field enhancements in and out the spheres as well as laser energy confinement at the particle substrate interface. The wide variety of features observed in the experiments open routes to fabricating nanomaterials.