The action of the enzyme CGTase on corn and potato starch was studied to understand the influence of starch structure and cyclodextrin (CD) production. Native and hydrolysed materials were analysed using multiple characterisation methods enabling coverage over more than six orders of magnitude in length-scale. The production of CD was greater for corn than potato but the relative abundance between different CD molecules was conserved. Structural differences were observed for all length scales investigated as a result of hydrolysis but to different extents between the starches. These observations were explained by differing modes of enzymatic attack between starch varieties. In corn, surface pores facilitated action of CGTase with hydrolysis generating limited changes in crystallinity and surface granule order. Hydrolysis of potato starch resulted in erosion at the granule surface, increase in surface order and overall crystallinity. Hydrolysis had minimal effect on the gelatinisation behaviour of both starches. Changes in the small-angle scattering due to CGTase confirmed the different mode of action of the enzyme between the two starches. Following hydrolysis, these changes in corn were consistent with preferential attack of the amorphous lamellae, while in potato, preferential hydrolysis of amorphous growth rings was indicated. These findings provide new insight into this industrially relevant enzyme and will assist in the optimisation of CGTase-based processing conditions for the development of novel products.