Aligned multiwalled carbon nanotube (CNT) arrays were prepared using chemical vapor deposition of C2H4 on Fe catalyst at 750 °C. CNT array height and alignment depends strongly on the duration of H2 pretreatment, with optimal height and alignment achieved using 10-15 min pretreatment. Small-angle X-ray scattering (SAXS) was used to quantify the alignment, distribution, and size of the CNTs in arrays produced from varying pretreatment times and the results correlated with microscopy measurements. SAXS analysis revealed that the higher section of the CNT arrays exhibited better alignment than the lower section. Combining these insights with transmission electron microscopy measurements of the CNT defects within each array enable a mechanism for the CNT growth to be proposed, where the loss of alignment arises from deformation of the CNTs during their growth. Gas permeation test across densified CNT arrays indicated that the alignment of the CNT array plays an important role in the gas transport, and that the gas diffusion across the well-aligned CNT arrays was enhanced by a factor of ~45, which is much more than that across the poorly aligned CNT arrays, with an enhancement factor of ~8.