An ultrafast laser machining system and method to form diffractive structures in optical fibers. The fiber is mounted with its longitudinal axis perpendicular to the beam path of the laser pulses. A region of the fiber is illuminated and then imaged with two cameras. These cameras are aligned substantially orthogonally. A position of the beam spot is determined. The beam spot is aligned to a starting position within the region. This position is within a portion of the fiber to be machined for which the beam path passes through the greatest length of material. The beam spot is scanned along a path designed to pass the beam spot through all of the portion to be machined such that the beam path does not pass through previously machined material. The laser pulses, which have a duration of less than about 1 ns, are generated as the beam spot is scanned.