Ultrafast pulse beams of light are used to direct-write three-dimensional index profiles in materials using the unique material changing capabilities of ultra-short (i.e. <10 picosecond) laser pulses. An existing waveguide or waveguide circuit fabricated by some technique (for example but not limited to photolithography, flame hydrolysis deposition, modified chemical vapor deposition, or ultra-fast laser pulse direct writing) is modified by altering the index of refraction (index trimming) in a localized region or different local regions of the waveguide structure. Index trimming is accomplished through the action of a focused laser beam (or multiple focused beams) consisting of one or more ultra-short laser pulses and is generally performed at a wavelength in which the material is transparent or weakly absorbing, to the fundamental wavelength of the beam of light. The trimmed index pattern is generated by, but not limited to, moving the focal position of the beam or by moving the sample (i.e. waveguide device) relative to a fixed beam focused. Trimming occurs only at or near the focus of the beam. The focus may be a beam waist or a reduced replica of the input beam as might be created by a simple lens or collection of lenses. Or the focus could be where a pattern encoded onto the phase front of the beam is imaged onto or into the sample as, for example, by use of a mask or diffractive optical element (DOE).