A laser atom probe (100) situates a counter electrode between a specimen mount and a detector (106), and provides a laser (116) having its beam (122) aligned to illuminate the specimen (104) through the aperture (110) of the counter electrode (108). The detector, specimen mount (102), and/or the counter electrode may be charged to some boost voltage and then be pulsed to bring the specimen to ionization. The timing of the laser pulses may be used to determine ion departure and arrival times allowing determination of the mass-to-charge ratios of the ions, thus their identities. Automated alignment methods are described wherein the laser is automatically directed to areas of interest.