Slit-shaped laser beams focused in bulk optical materials can realize embedded waveguides with circular cross sections consisting of positive index change type I traces. In these kinds of waveguide traces, a peculiar periodical refractive index modulation was observed in type I waveguides with two different femtosecond lasers. The direction of refractive index modulation can be controlled with the slit configuration, and its period can be controlled by mechanical perturbation of the stages and the scanning speed. We argue that platform perturbation and dynamical thermal transport processes during the scan are generating factors in the appearance of this modulation. The embedded microstructures in waveguides can provide spectrum modulation, which may have potential applications in optical sensing, filtering, and phase control.