This disclosure includes a system for aligning an unmounted head gimbal assembly (HGA) comprising a platform for a base plate of the HGA. The platform defines an X-Y plane. The system further comprises a compliant alignment pin extending beyond the platform in a Z-dimension perpendicular to the X-Y plane. The compliant alignment pin includes a tapered portion having a maximum diameter larger than a diameter of a boss hole in the base plate of the HGA. The compliant alignment pin is deflectable in the Z-dimension to allow the base plate of the HGA to register with the platform. The system further comprises a second alignment pin extending beyond the platform in the Z-dimension. The second alignment pin is configured to register with an HGA reference feature of the HGA when the boss hole of the HGA registers with the compliant alignment pin to precisely align the HGA relative to the compliant alignment pin and the second alignment pin.