We detail the monitoring of amorphous carbon deposition during thermal chemical vapour deposition of carbon nanotubes and propose a contamination-less process to integrate high-quality single-walled carbon nanotubes into micro-electromechanical systems. The amorphous content is evaluated by confocal micro-Raman spectroscopy and by scanning/transmission electron microscopy. We show how properly chosen process parameters can lead to successful integration of single-walled nanotubes, enabling nano-electromechanical system synthesis.