A method for forming a via in a sapphire substrate with a laser machining system that includes an ultrafast pulsed laser source. The sapphire substrate is provided. Pulses of laser light are substantially focused to a beam spot on the first surface of the sapphire substrate such that each focused pulse of laser light ablates a volume of the sapphire substrate having a depth less than the substrate thickness. The beam spot of the focused laser light pulses is scanned over a via portion of the first surface of the sapphire substrate. The sapphire substrate is moved in a direction substantially normal to the first surface to control the volume of the sapphire substrate ablated by each pulse of laser light to be substantially constant. The pulsing and scanning steps are repeated until the via is formed extending from the first surface to the second surface of the sapphire substrate.