Ultrafast Bessel beams are ideal sources for high aspect ratio submicron structuring applications because of their nondiffracting nature and higher stability in nonlinear propagation. We report here on the interaction of ultrafast Bessel beams at various laser energies and pulse durations with transparent materials (fused silica) and define their impact on photoinscription regimes, i.e., formation of positive and negative refractive index structures. The laser pulse duration was observed to be key in deciding the type of the structures via excitation efficiency. To understand the relevant mechanisms for forming these different structures, the free carrier behavior as a function of laser pulse duration and energy was studied by capturing instantaneous excitation profiles using time-resolved microscopy. Time-resolved imaging and simulation studies reveal that low carrier densities are generated for ultrashort pulses, leading to soft positive index alterations via presumably nonthermally induced structural transitions involving defects. On the other hand, the high free carrier density generation in the case of longer pulse durations leads to hydrodynamic expansion, resulting in high aspect ratio submicron-size wide voids. Delayed ionization, carrier defocusing, and lower nonlinear effects are responsible for the confinement of energy, resulting in efficient energy deposition on-axis.