The next generation instrument for ground-based gamma-ray astronomy will be the Cherenkov Telescope Array (CTA), consisting of approximately 100 telescopes in three sizes, built on two sites with one each in the Northern and Southern Hemi- spheres. Up to 40 of these will be Medium Size Telescopes (MSTs) which will dominate sensitivity in the core energy range. Since 2012, a full size mechanical prototype for the modified 12 m Davies-Cotton design MST has been in operation in Berlin. This doc- ument describes the techniques which have been implemented to calibrate and optimise the mechanical and optical performance of the prototype, and gives the results of over three years of observations and measurements. Pointing calibration techniques will be discussed, along with the development of a bending model, and calibration of the CCD cameras used for pointing measurements. Additionally alignment of mirror segments using the Bokeh method is shown.
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