The EU gyrotron for the ITER Electron Cyclotron (EC) heating system has been developed in coordinated efforts of the EGYC Consortium, Thales ED (TED) and Fusion for Energy (F4E) and under the supervision of ITER Organization Central Team. After the successful verification of the design of the 1MW, 170 GHz hollow cylindrical cavity gyrotron operating at the nominal TE32,9 mode with a short pulse gyrotron prototype at KIT, an industrial CW gyrotron prototype was manufactured by TED and tested at similar to 0.8 MW output power and 180 s pulse duration, which is the limit of the HV power supply currently available at KIT. The experiments are being continued at SPC in 2018 to extend further the pulse duration, taking advantage of the existing CW full-power capabilities of the gyrotron test facility recently upgraded for the FALCON project. The gyrotron cavity interaction is very sensitive to the alignment of the internal mechanical parts of the gyrotron tube with the magnetic field generated by the superconducting magnet within a typical range of 0.2 - 0.5 mm. The control of the tolerances and deformations becomes therefore critical to achieving the target performances. With the EU gyrotron prototype it was possible to adjust the alignment of the gyrotron tube with respect to the magnetic field axis during the installation and commissioning phase. The actual shift and tilt movements were verified using advanced metrology methods such as photogrammetry. In this paper, the alignment control techniques and procedures will be discussed also in view of enhancing the reproducibility of gyrotron performance during series production.