Alkali-free borosilicate glasses are one of the most used dielectric platforms for ultrafast laser inscribed integrated photonics. Femtosecond laser written waveguides in commercial Corning Eagle 2000, Corning Eagle XG and Schott AF32 glasses were analyzed. They were studied in depth to disclose the dynamics of waveguide formation. We believe that the findings presented in this paper will help bridge one of the major and important gaps in understanding the ultrafast light-matter interaction with alkali-free boroaluminosilicate glass. It was found that the waveguides are formed mainly due to structural and elemental reorganization upon laser inscription. Aluminum along with alkaline earth metals were found to be responsible for the densification and silicon being the exchanging element to form a rarefied zone. Strong affinity towards alkaline earth elements to form the densified zone for waveguides written with high feed rate (>200 mm/min) were identified and explained. Finally we propose a plausible solution to form positive refractive index change waveguides in different glasses based on current and previous reports.