Single-shot femtosecond laser ablation experiments with linearly and circularly polarized light were conducted in order to investigate the morphological characteristics of surface nanostructures in lithium borate crystals and glasses, a strontium borate crystal, lanthanide containing borate crystals, and aluminate silicate crystals: Li2B4O7 (LTB) and LiB3O5 (LBO) crystals and Li2O⋅2B2O3 (LTB) and Li2O⋅3B2O3 (LBO) glasses; SrB4O7 (SBO) crystal; Li6Gd(BO3)3 (LGB) and LaSc3(BO3)4 (LSB) crystals; and Ca2Al2SiO7 (CAS) and CaSrAl2SiO7 (CSAS) crystals. In the present study, the material and laser polarization dependance of the morphology of nanoholes was examined in these crystals and glasses. A single nanohole or two holes (a primary hole and a secondary hole) were observed in the borate and aluminate silicate crystals. The size of the nanohole is not restricted by the diffraction limit but instead is dependent on the laser fluence and the materials. It is suggested that the formation of these secondary nanoholes in the studied crystals is attributed to a spontaneous reshaping of the incoming Gaussian pulse into a Gaussian–Bessel pulse. In the LTB and LBO crystals, nanoholes (both primary and secondary holes) with subwavelength sides exhibit a quadrilateral (approximately square or rectangular) morphology, regardless of linear or circular polarization. The sides of the quadrilateral nanoholes lie approximately in the {h h 0} planes on the LTB crystal and in the ({h 0 0} and {0 0 l}) planes on the LBO crystal. We found that the nanohole morphology did not reflect the spatial distribution of the laser intensity. These phenomena were the first observations on the anisotropic morphology of nanoholes. These morphologies do not correspond to the circular symmetric pattern of the Gaussian intensity distribution of the incoming laser beam. This is contrary to the expectations based on the generally accepted laser ablation mechanism. The quadrilateral nanoholes could be an inherent morphology in the LTB and LBO crystals. The morphology of the quadrilateral holes in the LTB and LBO crystals is considered to reflect the continuous BO33− and/or BO45− network structure in their respective tetragonal or orthorhombic unit cells, in which self-tapped excitons are formed in an initial process under multiphoton excitation. In contrast, the SBO, LGB, LSB, CAS, and CSAS crystals and the LTB and LBO glasses exhibit circular nanoholes with subwavelength diameters independent of the laser polarization, the structure, or the composition. The isotropic morphology of nanoholes in these samples reflects the circular pattern of the Gaussian intensity profile of the focused laser beam.