The formation of periodic surface structures is a general effect of femtosecond laser irradiation of solid targets showing promising interest in material science and technology. However, the experiments are typically carried out in air, a condition in which the target surface becomes densely decorated with nanoparticles that can influence the formation of the surface structures in the early stage of the irradiation process. Here we report an investigation of structures generation on a silicon surface irradiated in vacuum (10-5 mbar) with a low number of laser pulses (N ≤ 10) that exploits several microscopy techniques (optical, atomic force, electron and Raman). Our analyses allow identifying the creation of silicon phase-change gratings consisting of alternating amorphous and crystalline periodic lines, with almost no material removal, located at the periphery of a shallow ablation crater. These gratings originate from two different kinds of defects: (i) the first is characterized by a peculiar lobed shape that is produced by the first few laser pulses; (ii) the second is provided by the one-dimensional, linear singularity defined by the ablation edge of the nascent crater. Both kind of defects lead to grating structures extending outwards the amorphous central area of the crater along the direction of the laser polarization. Comparative analysis with the surface formed in air, in the same experimental conditions, evidences the important role played by nanoparticles densely decorating the target in air and the striking variation occurring in vacuum.