The Dark Energy Spectroscopic Instrument (DESI) is under construction to measure the expansion history of the universe using the Baryon Acoustic Oscillation (BAO) technique. The spectra of 35 million galaxies and quasars over 14000 deg2 will be measured during the life of the experiment. A new prime focus corrector for the KPNO Mayall telescope will deliver light to 5000 robotically positioned optic fibres. The fibres in turn feed ten broadband spectrographs. Proper alignment of focal plate structure, mainly consisting of a focal plate ring (FPR) and ten focal plate petals (FPP), is crucial in ensuring minimal loss of light in the focal plane. A coordinate measurement machine (CMM) metrology-based approach to alignment requires comprehensive characterisation of critical dimensions of the petals and the ring, all of which were 100% inspected. The metrology data not only served for quality assurance (QA), but also, with careful modelling of geometric transformations, informed the initial choice of integration accessories such as gauge blocks, pads, and shims. The integrated focal plate structure was inspected again on a CMM, and each petal was adjusted according to the updated focal plate metrology data until all datums were extremely close to nominal positions and optical throughput nearly reached the theoretically best possible value. This paper presents our metrology and alignment methodology and complete results for twelve official DESI petals. The as-aligned, total RMS optical throughput for 6168 positioner holes of twelve production petals was indirectly measured to be 99:88±0.12%, well above the 99.5% project requirement. The successful alignment fully demonstrated the wealth of data, reproducibility, and micron-level precision made available by our CMM metrology-based approach.