Employing optical phase-contrast microscopy we study the morphology of ultrashort pulsed laser-induced modifications in bulk fused silica and in other optical transparent materials for different conditions of irradiation. The influence of the input pulse energy, focusing depth, and number of pulses per site is investigated in order to establish optimal irradiation conditions for direct writing of waveguiding elements. The results obtained suggest that an increase of the refractive index is systematically accompanied by a region of lower index of refraction along the optical axis, presumably due to micro-explosion in the high energy-exposed regions, and the locations of this region is material dependent. Nevertheless, the creation of an hypothetical void in the interaction zone does not allow a complete explanation of the modifications observed and other mechanisms have to be invoked to explain the presence of regions with higher index of refraction. Different interaction regimes with respect to the input energy and to the number of shots per site can be established from these observations, emphasizing the role of nonlinear pulse propagation and plasma generation. To complement the experimental observations we simulate the propagation of an ultrashort laser pulse in bulk silica using the non-linear Schrödinger equation and determine the distribution of energy along the propagation axis. The results are in good agreement with the experimental observations and provides insights into the mechanisms controlling the interaction between ultrashort laser pulses and transparent materials.