Single-walled carbon nanotubes (SWNT) are a promising material for nanoelectronics because of their physical and electrical properties. To this end, they should be synthesized with controlled orientation, alignment, yield and electronic type. Chemical vapor deposition (CVD) is widely used method for growing horizontally aligned SWCNT on selectively cut single crystal substrates such as ST-cut quartz. Thermal annealing of the substrates prior the CVD process is an often implemented step to improve yield. Nevertheless, the role of the annealing step has not been fully investigated. Here, we systematically investigate the eect of the annealing step on the morphology of the ST-cut quartz substrates, in order to provide excellent conditions for high nucleation yields and growth of long tubes . Also, the surface morphology is shown to aect the catalyst nanoparticles size distribution which aects their propensity to nucleate SWNT. The ratio of the catalyst metal mix (Fe:Co) is shown to be a less important parameter. The successful transfer of the aligned SWCNTs onto other substrates without incurring damage or misalignment is also demonstrated.