We demonstrate the formation of nanostructures inside the microholes on soda-lime glass surface by irradiation with femtosecond laser pulses. Self-organized periodic nanogratings, oriented perpendicular to the laser polarization, are observed at the bottom of the microholes. The period of the nanogratings are ranging from 170 nm to 200 nm. We also report the formation of nano-ripples on the side walls of the microholes, the period of which are independent of the laser fluence and the number of laser pulses. Nano-cones, with a diameter varied from 100 nm to 250 nm, are also discovered on the sidewalls of the microholes. Randomly distributed spherical-shaped nanostructures with a diameter ranging from 10 nm to 60 nm are also evident inside the microholes, especially, on the top of the nano-ripples and nano-cones. We also describe, briefly, the dependence of various micro/nano-structures on the laser fluence and the number of applied laser pulses in each spot. Finally, we explain the formation mechanism of all of the micro/nano-scale features, produced during our experiment.