Embodiments of methods and apparatus for aligning a probe card assembly in a test system are provided herein. In some embodiments, an apparatus for testing devices may include a probe card assembly having a plurality of probes, each probe having a tip for contacting a device to be tested, and having an identified set of one or more features that are preselected in accordance with selected criteria for aligning the probe card assembly within a prober after installation therein. In some embodiments, the identity of the identified set of one or more features may be communicated to the prober to facilitate a global alignment of the probe card assembly that minimizes an aggregate misalignment of all of the tips in the probe card assembly.