Femtosecond laser inscription allows straightforward manufacturing of glass planar lightwave circuits such as waveguides, interferometers, directional couplers, resonators and more complex structures. Fiber alignment structures are needed to facilitate communication with the glass planar lightwave circuit. In this study, a technique is described to create optical waveguides and alignment structures in the same laser exposure step. Using an industrial ytterbium-doped 1030 nm fiber laser pulses of 400 fs were focused into glass with a 0.4 NA objective causing permanent alteration of the material. Depending on laser parameters this modification allows direct writing of waveguides or the creation of channels after exposing the irradiated volumes to an etchant such as KOH. Writing of channels and waveguides with different laser powers, frequencies, polarisations, stage translation speeds and scan densities were investigated in fused silica and borosilicate glass. Waveguides with controlled dimensions were created, as well as etched U-grooves with a diameter of 126 μm and a sidewall roughness Ra of 255 nm. Cut back measurements were performed giving a waveguide propagation loss of 1.1 dB/cm in borosilicate glass. A coupling loss of 0.7 dB was measured for a transition between the waveguide and standard single mode fiber at 1550 nm, using index matching liquid. The described technique eliminates active alignment requirements and is useful for many applications such as microfluidic sensing, PLCs, fan-out connectors for multicore fibers and quantum optical networks.